Mesothelin antibody protein fusions and methods of use

ABSTRACT

The invention relates to fusion proteins comprising a stress protein fused with an engineered antibody or fragment that binds to mesothelin, or a stress protein fused with a biotin-binding protein in combination with a biotinylated engineered antibody or fragment that binds to mesothelin. The invention also relates to fusion proteins comprising a stress protein fused with an antibody binding protein in combination with an engineered antibody or fragment that binds to mesothelin. The invention also relates to fusion proteins comprising an engineered antibody or fragment that binds specifically to mesothelin fused in frame with a biotin binding protein. The invention also provides fusion proteins comprising an engineered antibody or fragment, that binds to mesothelin, fused with an antibody binding protein. The invention also relates to methods of using fusion proteins of the invention to induce an immune response to mesothelin and to treat disease.

RELATED APPLICATIONS/PATENTS & INCORPORATION BY REFERENCE

This application is a continuation of U.S. application Ser. No. 12/291,104, filed on Nov. 6, 2008, issued as U.S. Pat. No. 7,943,133 on May 17, 2011. The entire teachings of the above application is incorporated herein by reference.

BACKGROUND OF THE INVENTION

Mesothelin is a differentiation antigen whose expression in normal human tissues is limited to mesothelial cells lining the pleura, pericardium and peritoneum. However, mesothelin is highly expressed in several human cancers, including mesotheliomas, pancreatic adenocarcinomas, ovarian cancers and lung adenocarcinomas. Mesothelin is an appropriate target for methods of disease prevention or treatment and antibodies specific for mesothelin, and vaccines comprising mesothelin are useful for prophylactic and therapeutic methods.

Classical monoclonal antibodies are currently produced in mammalian cells. Drawbacks of this method of production include the difficulty of producing and selecting appropriate clones, and the expense of culturing mammalian cells. The “next generation” of monoclonal antibodies are being engineered in E. coli. Recently, microbial expression of V_(H) and V_(L) domains tethered together by polypeptide linkers has created the capability of generating engineered “mini-antibodies.” These mini-bodies can be generated in E. coli in a virtually combinatorial fashion. These artificially created Fab or single chain Fv (scFv) can be linked together to form multimers, e.g., diabodies, triabodies and tetrabodies. Although they are capable of binding to antigens with almost antibody-like efficiency, these engineered, Fc deficient mini-antibodies lack the ability to interact with antigen presenting cells and are poorly immunogenic. Existing solutions to the lack of immunogenicity of engineered antibodies involve directing one of the antigen binding sites to bind directly with immune cells. This brings them in apposition, but does not result in the same MHC class I priming as would be observed for a monoclonal antibody.

Immunization with vaccines remains a cornerstone of protection against threat of disease and infection. The key difficulty in vaccine development is rapidly matching a vaccine, or antitoxin, to a specific threat. Current vaccine development strategies rely on the identification and characterization of antigens that can be targeted to successfully eradicate infection or disease. Current vaccine development strategies are time- and labor-intensive and can only commence once a threat emerges. Such strategies are also impractical for generating personalized vaccines to combat disease for which target antigens varies among individuals. Current vaccine development strategies are therefore insufficient if a new and serious threat were to emerge, for which sufficient time were not available to identify and characterize target antigens before such a threat could be contained. Current vaccine development strategies are also insufficient for generating personalized vaccines for the general population.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 presents a diagram of an MTBHSP70(C) Hinge Anti-mesothelin scFv fusion protein.

FIG. 2 presents the nucleic (SEQ ID NO: 12) and amino acid (SEQ ID NO: 13) sequence of an MTBHSP70 (C) Hinge anti-mesothelin scFv fusion protein.

FIG. 3 presents a diagram of an MTBHSP70(N) Hinge Anti-mesothelin scFv fusion protein.

FIG. 4 presents the nucleic (SEQ ID NO: 14) and amino acid (SEQ ID NO: 15) sequence of an MTBHSP70 (N) hinge anti-mesothelin scFv fusion protein.

FIG. 5 presents a diagram of an HuHSP70(C) Hinge Anti-mesothelin scFv fusion protein.

FIG. 6 presents the nucleic (SEQ ID NO: 16) and amino acid (SEQ ID NO: 17) sequence of HuHSP70(C) hinge anti-mesothelin scFv.

FIG. 7 presents the diagram of an HuHSP70 (N) Hinge Anti-mesothelin scFv fusion protein.

FIG. 8 presents the nucleic (SEQ ID NO: 18) and amino acid (SEQ ID NO: 19) sequence of HuHSP70 (N) hinge anti-mesothelin scFv.

FIG. 9 presents a diagram of an MTBHSP70 (C) linker mesothelin peptide fusion protein.

FIG. 10 presents the nucleic (SEQ ID NO: 20) and amino acid (SEQ ID NO: 21) sequence of MTBHSP70 (C) linker mesothelin peptide fusion protein.

FIG. 11 presents a diagram of an MTBHSP70 (N) linker mesothelin peptide fusion protein.

FIG. 12 presents the nucleic (SEQ ID NO: 22) and amino acid (SEQ ID NO: 23) sequence of MTBHSP70 (N) linker mesothelin peptide.

FIG. 13 presents a diagram of an HuHSP70 (C) linker mesothelin peptide.

FIG. 14 presents the nucleic (SEQ ID NO: 24) and amino acid (SEQ ID NO: 25) sequence of HuHSP70 (C) linker mesothelin peptide fusion protein.

FIG. 15 presents a diagram of an HuHSP70 (N) linker mesothelin peptide.

FIG. 16 presents the nucleic (SEQ ID NO: 26) and amino acid (SEQ ID NO: 27) sequence of HuHSP70 (N) linker mesothelin peptide.

FIG. 17 A-E presents fusion proteins according to the invention (6×His disclosed as SEQ ID NO: 28).

FIG. 17 A-E presents fusion proteins according to the invention.

FIG. 18A presents a diagram of an hsp70-scFV fusion protein construct.

FIG. 18 B presents a diagram of an hsp70-scFV protein.

FIG. 19 A presents a diagram of an hsp70-avidin fusion protein construct.

FIG. 19 B presents a diagram of an hsp70-avidin protein.

FIGS. 20A and B depict the full-length polypeptide sequences of HSP70 from Mycobacterium tuberculosis (SEQ ID NO: 29) HSP70 and Mycobacterium bovis (SEQ ID NO: 30) HSP70, respectively.

SUMMARY OF THE INVENTION

The invention provides a fusion protein comprising a stress protein fused in frame with an engineered antibody or fragment thereof, that binds specifically to mesothelin.

The invention also provides a fusion protein comprising a stress protein fused in frame with a biotin-binding protein in combination with a biotinylated engineered antibody or fragment thereof, that binds specifically to mesothelin.

The invention also provides a fusion protein comprising a stress protein fused in frame with an antibody binding protein in combination with an engineered antibody or fragment thereof, that binds specifically to mesothelin.

The invention also provides a fusion protein comprising an engineered antibody or fragment thereof, that binds specifically to mesothelin fused in frame with a biotin binding protein.

The invention also provides a fusion protein comprising an engineered antibody or fragment thereof, that binds specifically to mesothelin fused in frame with an antibody binding protein.

In one embodiment the biotin-binding protein is selected from the group consisting of: avidin, streptavidin, and neutravidin.

In another embodiment the biotin-binding protein is non-covalently bound to a biotinylated component.

In another embodiment the biotin binding protein is non-covalently bound to four biotinylated components, and further wherein at least two of the four biotinylated components are not identical.

In another embodiment, at least one of the four biotinylated components is a costimulatory molecule.

In another embodiment, the antibody binding protein is selected from the group consisting of: protein A, protein G, protein A/G and protein L.

In another embodiment the fusion protein further comprises a linker.

In another embodiment, the linker comprises an amino acid sequence selected from the group consisting of: GGSSRSS (SEQ ID NO: 1), (GGGSGGG)×4 (SEQ ID NO: 2) or GGGGSGGGGSGGGGS (SEQ ID NO: 3).

The invention also provides for an isolated nucleic acid encoding the fusion protein of the invention.

The invention also provides for an expression vector comprising a nucleic acid encoding the fusion protein of the invention.

The invention also provides for a cell comprising an expression vector comprising a nucleic acid encoding the fusion protein of the invention.

The invention also provides for a pharmaceutical composition comprising an effective amount of a fusion protein of the invention, and a pharmaceutically acceptable carrier.

The invention also provides for an immunogenic composition or vaccine comprising a fusion protein of the invention.

The invention also provides for a kit comprising a composition or vaccine comprising a fusion protein of the invention, and packaging means thereof.

In one embodiment, the kit further comprises instructions for performing any of the methods of the claimed invention, including a method for inducing an immune response to mesothelin, and a method of treating a disease.

The invention also provides for a method for inducing an immune response to mesothelin in a subject comprising administering to the subject a fusion protein comprising a stress protein fused in frame with an engineered antibody or fragment thereof, that binds specifically to mesothelin to induce an immune response.

The invention also provides for a method of treating a disease in a subject, comprising administering to the subject a fusion protein comprising a stress protein fused in frame with an engineered antibody or fragment thereof, that binds specifically to mesothelin to treat a disease.

The invention also provides for a method for inducing an immune response in a subject, comprising administering to said subject a fusion protein comprising a stress protein fused in frame with a biotin-binding protein in combination with a biotinylated engineered antibody or fragment thereof, that binds specifically to mesothelin, to induce an immune response.

The invention also provides for a method of treating a disease in a subject, comprising administering to said subject a fusion protein comprising a stress protein fused in frame with a biotin-binding protein in combination with a biotinylated engineered antibody or fragment thereof, that binds specifically to mesothelin, to treat a disease.

The invention also provides for a method for inducing an immune response in a subject, comprising administering to said subject a fusion protein comprising an engineered antibody or fragment thereof, that binds specifically to mesothelin, fused in frame with a biotin binding protein to induce an immune response.

The invention also provides for a method of treating a disease in a subject, comprising administering to said subject a fusion protein comprising an engineered antibody or fragment thereof, that binds specifically to mesothelin fused in frame with a biotin binding protein to treat a disease.

In one embodiment, the claimed methods are performed with a biotin-binding protein selected from the group consisting of avidin, streptavidin, and neuravidin.

In another embodiment the biotin-binding protein is non-covalently bound to a biotinylated component.

In another embodiment, the biotin binding protein is non-covalently bound to four biotinylated components, and further wherein at least two of the four biotinylated components are not identical.

In another embodiment, at least one of the four biotinylated components is a costimulatory molecule.

In another embodiment, the fusion protein further comprises a linker.

In another embodiment, the linker comprises an amino acid sequence selected from the group consisting of: GGSSRSS (SEQ ID NO: 1), (GGGSGGG)×4 (SEQ ID NO: 2) or GGGGSGGGGSGGGGS (SEQ ID NO: 3).

The invention also provides for a method for inducing an immune response in a subject, comprising administering to said subject a fusion protein comprising a stress protein fused in frame with an antibody binding protein in combination with an engineered antibody or fragment thereof, that binds specifically to mesothelin, to induce an immune response.

The invention also provides for a method of treating a disease in a subject, comprising administering to said subject a fusion protein comprising a stress protein fused in frame with an antibody binding protein in combination with an engineered antibody or fragment thereof, that binds specifically to mesothelin, to treat a disease.

The invention also provides for a method for inducing an immune response in a subject, comprising administering to said subject a fusion protein comprising an engineered antibody or fragment thereof, that binds specifically to mesothelin fused in frame with an antibody binding protein to induce an immune response.

The invention also provides for a method of treating a disease in a subject, comprising administering to said subject a fusion protein comprising an engineered antibody or fragment thereof, that binds specifically to mesothelin fused in frame with an antibody binding protein to treat a disease.

In one embodiment, the claimed methods are performed with an antibody binding protein selected from the group consisting of: protein A, protein G, protein A/G and protein L.

In another embodiment, the fusion protein comprises a linker.

In another embodiment, the linker comprises an amino acid sequence selected from the group consisting of: GGSSRSS (SEQ ID NO: 1), (GGGSGGG)×4 (SEQ ID NO: 2) or GGGGSGGGGSGGGGS (SEQ ID NO: 3).

DETAILED DESCRIPTION OF THE INVENTION

The invention relates to novel proteins that illicit an immune response to mesothelin and their methods of use.

Definitions

The singular forms “a”, “an”, and “the” include plural references unless the context clearly dictates otherwise.

As used herein “mesothelin” refers to a differentiation antigen whose expression in normal human tissues is limited to mesothelial cells lining the pleura, pericardium and peritoneum. However, mesothelin is highly expressed in several human cancers, including mesotheliomas, pancreatic adenocarcinomas, ovarian cancers and lung adenocarcinomas. The mesothelin gene encodes a precursor protein of 71 kDa that is processed to a 31 kDa shed protein called megakaryocyte potentiating factor (MPF) and a 40 kDa fragment, mesothelin, that is attached to the cell membrane by a glycosyl-phosphatidylinositol (GPI) anchor.

There are three (3) variants of mesothelin: soluble mesothelin-1, a unique mesothelin-2 transcript, and a mesothelin-3 variant with an extended C-terminus Mesothelin-1 is found in pleura, pericardium and peritoneum and on surface epithelium of the ovaries, tonsils, and fallopian tubes (Ordonez, 2003). Mesothelin is also overexpressed in mesotheliomas, pancreatic adenocarcinomas, and squamous cell carcinomas of the head, neck, lung, esophagus, cervix, and vulva (Chang and Pastan 1992, 1996; Frierson et al. 2003).

The term “administering” includes any method of delivery of a compound of the present invention, including but not limited to, a pharmaceutical composition or therapeutic agent, into a subject's system or to a particular region in or on a subject, including systemic or localized administration. The phrases “systemic administration,” “administered systemically,” “peripheral administration” and “administered peripherally” as used herein mean the administration of a compound, drug or other material other than directly into the central nervous system, such that it enters the patient's system and, thus, is subject to metabolism and other like processes, for example, subcutaneous administration. “Parenteral administration” and “administered parenterally” means modes of administration other than enteral and topical administration, usually by injection, and includes, without limitation, intravenous, intramuscular, intralesional, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intra-articular, subcapsular, subarachnoid, intraspinal and intrasternal injection, oral, epidural, intranasal and infusion.

The term “amino acid” is intended to embrace all molecules, whether natural or synthetic, which include both an amino functionality and an acid functionality and capable of being included in a polymer of naturally-occurring amino acids. Exemplary amino acids include naturally-occurring amino acids; analogs, derivatives and congeners thereof; amino acid analogs having variant side chains; and all stereoisomers of any of any of the foregoing. The names of the natural amino acids are abbreviated herein in accordance with the recommendations of IUPAC-IUB.

The term “antibody” refers to an immunoglobulin, derivatives thereof which maintain specific binding ability, and proteins having a binding domain which is homologous or largely homologous to an immunoglobulin binding domain. These proteins may be derived from natural sources, or partly or wholly synthetically produced. An antibody may be monoclonal or polyclonal. The antibody may be a member of any immunoglobulin class, including any of the human classes: IgG, IgM, IgA, IgD, IgE and IgY. In exemplary embodiments, antibodies used with the methods and compositions described herein are derivatives of the IgG class. The term “antibody” also includes an antibody fragment as defined herein.

The term “antibody fragment” refers to any derivative of an antibody which is less than full-length. In exemplary embodiments, the antibody fragment retains at least a significant portion of the full-length antibody's specific binding ability. Examples of antibody fragments include, but are not limited to, Fab, Fab′, F(ab′)₂, scFv, Fv, dsFv diabody, and Fd fragments. The antibody fragment may be produced by any means. For instance, the antibody fragment may be enzymatically or chemically produced by fragmentation of an intact antibody, it may be recombinantly produced from a gene encoding the partial antibody sequence, or it may be wholly or partially synthetically produced. The antibody fragment may optionally be a single chain antibody fragment. Alternatively, the fragment may comprise multiple chains which are linked together, for instance, by disulfide linkages. The fragment may also optionally be a multimolecular complex. A functional antibody fragment will typically comprise at least about 50 amino acids and more typically will comprise at least about 200 amino acids.

The term “Fab fragment” refers to a fragment of an antibody comprising an antigen-binding site generated by cleavage of the antibody with the enzyme papain, which cuts at the hinge region N-terminally to the inter-H-chain disulfide bond and generates two Fab fragments from one antibody molecule.

The term “F(ab′)2 fragment” refers to a fragment of an antibody containing two antigen-binding sites, generated by cleavage of the antibody molecule with the enzyme pepsin which cuts at the hinge region C-terminally to the inter-H-chain disulfide bond.

The term “Fc fragment” refers to the fragment of an antibody comprising the constant domain of its heavy chain.

The term “Fv fragment” refers to the fragment of an antibody comprising the variable domains of its heavy chain and light chain.

The term “engineered antibody” refers to a recombinant molecule that comprises at least an antibody fragment comprising an antigen binding site derived from the variable domain of the heavy chain and/or light chain of an antibody and may optionally comprise the entire or part of the variable and/or constant domains of an antibody from any of the Ig classes (for example IgA, IgD, IgE, IgG, IgM and IgY). Examples of engineered antibodies include enhanced single chain monoclonal antibodies and enhanced monoclonal antibodies. Examples of engineered antibodies are further described in PCT/US2007/061554, the entire contents of which are incorporated herein by reference. An “engineered antibody” includes an engineered antibody fragment, according to the method of the invention, and as defined herein.

The term “single chain variable fragment or scFv” refers to an Fv fragment in which the heavy chain domain and the light chain domain are linked. One or more scFv fragments may be linked to other antibody fragments (such as the constant domain of a heavy chain or a light chain) to form antibody constructs having one or more antigen recognition sites.

The term “multivalent antibody” refers to an antibody or engineered antibody comprising more than one antigen recognition site. For example, a “bivalent” antibody has two antigen recognition sites, whereas a “tetravalent” antibody has four antigen recognition sites. The terms “monospecific”, “bispecific”, “trispecific”, “tetraspecific”, etc. refer to the number of different antigen recognition site specificities (as opposed to the number of antigen recognition sites) present in a multivalent antibody. For example, a “monospecific” antibody's antigen recognition sites all bind the same epitope. A “bispecific” antibody has at least one antigen recognition site that binds a first epitope and at least one antigen recognition site that binds a second epitope that is different from the first epitope. A “multivalent monospecific” antibody has multiple antigen recognition sites that all bind the same epitope. A “multivalent bispecific” antibody has multiple antigen recognition sites, some number of which bind a first epitope and some number of which bind a second epitope that is different from the first epitope.

The term “epitope” refers to the region of an antigen to which an antibody binds preferentially and specifically. A monoclonal antibody binds preferentially to a single specific epitope of a molecule that can be molecularly defined. In the present invention, multiple epitopes can be recognized by a multispecific antibody.

An “antigen” refers to a target of an immune response induced by a composition described herein. An antigen may be a protein antigen and is understood to include an entire protein, fragment of the protein exhibited on the surface of a virus or an infected, foreign, or tumor cell of a subject, as well as a peptide displayed by an infected, foreign, or tumor cell as a result of processing and presentation of the protein, for example, through the typical MHC class I or II pathways. Examples of such foreign cells include bacteria, fungi, and protozoa. Examples of bacterial antigens include Protein A (PrA), Protein G (PrG), and Protein L (PrL).

The term “antigen binding site” refers to a region of an antibody or fragment thereof, that specifically binds an epitope on an antigen.

The term “biotin-binding protein” refers to a protein, which non-covalently binds to biotin. A biotin-binding protein may be a monomer, dimer, or tetramer, capable of forming monovalent, divalent, or tetravalent pharmaceutical compositions, respectively, as described herein. Non-limiting examples include anti-biotin antibodies, avidin, streptavidin, and neutravidin. The avidin may comprise mature avidin, or a sequence that is at least 50%, 60%, 70%, 80%, 85%, 90%, 95%, or 99% identical to the sequence identified by NCBI Accession No. NP_(—)990651. The streptavidin may comprise, for example, a sequence that is at least 50%, 60%, 70%, 80%, 85%, 90%, 95%, or 99% identical to the sequence identified by of NCBI Accession No. AAU48617. The term “biotin-binding protein” is intended to encompass wild-type and derivatives of avidin, streptavidin, and neutravidin, which form monomers, dimers or tetramers. Examples of such derivatives are set forth below and also described in Laitinen, O. H. (2007), “Brave New (Strept)avidins in Biotechnology,” Trends in Biotechnology 25 (6): 269-277 and Nordlund, H. R. (2003), “Introduction of histidine residues into avidin subunit interfaces allows pH-dependent regulation of quaternary structure and biotin binding,” FEBS Letters 555: 449-454, the contents of both of which are expressly incorporated herein by reference.

The term “costimulatory molecule” as used herein includes any molecule which is able to either enhance the stimulating effect of an antigen-specific primary T cell stimulant or to raise its activity beyond the threshold level required for cellular activation, resulting in activation of naive T cells. Such a costimulatory molecule can be a membrane-resident receptor protein.

In this disclosure, “comprises,” “comprising,” “containing” and “having” and the like have the open-ended meaning ascribed to them in U.S. Patent law and mean “includes,” “including,” and the like.

The term “effective amount” refers to that amount of a compound, material, or composition which is sufficient to effect a desired result. An effective amount of a compound can be administered in one or more administrations.

A “fusion protein” or “fusion polypeptide” refers to a hybrid polypeptide which comprises polypeptide portions from at least two different polypeptides. A “fusion protein” as defined herein, is a fusion of a first amino acid sequence (protein) comprising, for example a stress protein of the invention, joined to a second amino acid sequence comprising an antibody or fragment thereof that binds specifically to mesothelin or a biotin-binding protein. A fusion protein also includes a fusion protein comprising a first amino acid sequence comprising a stress protein, and a second amino sequence comprising a biotin binding protein. A fusion protein also includes a fusion protein comprising a first amino acid sequence comprising a stress protein and second amino acid sequence comprising an antibody binding protein. A fusion protein also includes a fusion protein comprising a first amino acid sequence comprising an antibody or fragment thereof that binds specifically to mesothelin and a second amino acid sequence comprising a biotin binding protein or an antibody binding protein.

The portions may be from proteins of the same organism, in which case the fusion protein is said to be “interspecies”, “intergenic”, etc. In various embodiments, the fusion polypeptide may comprise one or more amino acid sequences linked to a first polypeptide. In the case where more than one amino acid sequence is fused to a first polypeptide, the fusion sequences may be multiple copies of the same sequence, or alternatively, may be different amino acid sequences. A first polypeptide may be fused to the N-terminus, the C-terminus, or the N- and C-terminus of a second polypeptide. Furthermore, a first polypeptide may be inserted within the sequence of a second polypeptide.

The term “linker” is art-recognized and refers to a molecule (including but not limited to unmodified or modified nucleic acids or amino acids) or group of molecules (for example, 2 or more, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more) connecting two compounds, such as two polypeptides. The linker may be comprised of a single linking molecule or may comprise a linking molecule and at least one spacer molecule, intended to separate the linking molecule and a compound by a specific distance.

A “spacer molecule” includes any amino acid segment that is not related to the two protein segments it separates. For example, in a fusion consisting of a stress protein and a biotin protein, a spacer molecule would consist of a stretch of amino acids that is unrelated to the proteins comprising the fusion protein. A “spacer molecule useful according to the invention includes neutral amino acids such as glycine, leucine, valine, alanine, rather than acidic or basic amino acids like aspartate, or arginine respectively.

“Gene construct” refers to a nucleic acid, such as a vector, plasmid, viral genome or the like which includes a “coding sequence” for a polypeptide or which is otherwise transcribable to a biologically active RNA (e.g., antisense, decoy, ribozyme, etc), may be transfected into cells, e.g. in certain embodiments mammalian cells, and may cause expression of the coding sequence in cells transfected with the construct. The gene construct may include one or more regulatory elements operably linked to the coding sequence, as well as intronic sequences, polyadenylation sites, origins of replication, marker genes, etc.

“Host cell” refers to a cell that may be transduced with a specified transfer vector. The cell is optionally selected from in vitro cells such as those derived from cell culture, ex vivo cells, such as those derived from an organism, and in vivo cells, such as those in an organism. It is understood that such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.

The term “including” is used herein to mean “including but not limited to”. “Including” and “including but not limited to” are used interchangeably.

The term “immunogenic” refers to the ability of a substance to elicit an immune response. An “immunogenic composition” or “immunogenic substance” is a composition or substance which elicits an immune response. An “immune response” refers to the reaction of a subject to the presence of an antigen, which may include at least one of the following: antibody production, inflammation, developing immunity, developing hypersensitivity to an antigen, the response of antigen specific lymphocytes to antigen, tolerance, and transplant or graft rejection.

As used herein, “an immune response to mesothelin” means, for example, a humoral or cellular response to mesothelin.

If a patient is mounting a humoral immune response to mesothelin, anti-mesothelin antibody titer is measured. A typical immunoassay consists of coating the wells of an immunoassay plate with mesothelin (for example by adding recombinant mesothelin or using a capture anti-mesothelin antibody) and then adding serial dilutions of patient serum to the wells. After washing away the sera, human immunoglobulins are detected with a conjugated anti-human immunoglobulin.

A cellular immune response is measured by using a cell-killing assay. Patients peripheral blood lymphocytes (PBL) are isolated and added at different ratios to a CHO cell line expressing mesothelin (non-transfected CHO cells or CHO cells transfected with a non-mesothelin construct are used as negative control). The mesothelin expressing CHO cells are transfected with a mesothelin construct and selected to express mesothelin on their surface. Killing is measured using radioactivity or release of a specific dye.

As used herein, “treating a disease” means reducing the amount of soluble mesothelin in the plasma of patients. Treating a disease also refers to reducing the tumor burden as measured by clinical means (for example by ecography or other methods known in the art. Treating a disease also refers to reducing tumor size/mass and/or prevention of metastases.

The enhanced mesothelin antibody as described herein, will reduce (eliminate) the tumor burden in patients diagnosed with ovarian cancer, meningiomas, gliomas and metastases to the leptomininges, mesotheliomas, adenocarcinoma of the uterus, malignant mesothelioma, pancreatic cancer and lung adenocarcinoma.

The term “isolated polypeptide” or “isolated protein” refers to a polypeptide, which may be prepared from recombinant DNA or RNA, or be of synthetic origin, some combination thereof, or which may be a naturally-occurring polypeptide, which (1) is not associated with proteins with which it is normally associated in nature, (2) is isolated from the cell in which it normally occurs, (3) is essentially free of other proteins from the same cellular source, (4) is expressed by a cell from a different species, or (5) does not occur in nature.

“Isolating” a polypeptide or protein refers to the process of removing a polypeptide from a tissue, cell or any mixture of polypeptides which are not polypeptides or proteins of interest. An isolated polypeptide or protein will be generally free from contamination by other polypeptides or proteins. An isolated polypeptide or protein can exist in the presence of a small fraction of other polypeptides or proteins which do not interfere with the utilization of the polypeptide or protein of interest. Isolated polypeptides or proteins will generally be at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% pure. In one embodiment, isolated polypeptides or proteins according to the invention will be at least 98% or 99% pure.

The term “isolated nucleic acid” refers to a polynucleotide of genomic, cDNA, synthetic, or natural origin or some combination thereof, which (1) is not associated with the cell in which the “isolated nucleic acid” is found in nature, or (2) is operably linked to a polynucleotide to which it is not linked in nature.

“Isolating” a nucleic acid refers to the process of removing a nucleic acid from a tissue, cell or any mixture of nucleic acids which are not nucleic acids of interest. An isolated nucleic acid will be generally free from contamination by other nucleic acids. An isolated nucleic acid can exist in the presence of a small fraction of other nucleic acids which do not interfere with the utilization of the nucleic acid of interest. Isolated nucleic acids will generally be at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% pure. In one embodiment, isolated polypeptides or proteins according to the invention will be at least 98% or 99% pure.

When referring to “polypeptide” herein, a person of skill in the art will recognize that a protein can be used instead, unless the context clearly indicates otherwise. A “protein” may also refer to an association of one or more polypeptides

The term “nucleic acid” refers to a polymeric form of nucleotides, either ribonucleotides or deoxynucleotides, a combination of ribo and deoxyribonucleotides or a modified form of either type of nucleotide. The terms should also be understood to include, as equivalents, analogs of either RNA or DNA made from nucleotide analogs, and, as applicable to the embodiment being described, single-stranded (such as sense or antisense) and double-stranded polynucleotides.

Unless the context clearly indicates otherwise, “protein,” “polypeptide,” and “peptide” are used interchangeably herein when referring to a gene expression product, e.g., an amino acid sequence as encoded by a coding sequence. A “protein” may also refer to an association of one or more proteins, such as an antibody. A “protein” may also refer to a protein fragment. A protein may be a post-translationally modified protein such as a glycosylated protein.

A “protein” according to the invention includes a protein wherein one or more (for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more) amino acids are not identical to the amino acids of the corresponding wild type protein. A “protein” according to the invention includes a protein wherein one or more (for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more) amino acids have been deleted as compared to the corresponding wild type protein. A “protein” according to the invention includes a protein wherein one or more (for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) amino acids have been added as compared the corresponding wild type protein.

By “gene expression product” is meant a molecule that is produced as a result of transcription of an entire gene or a portion of a gene. Gene products include RNA molecules transcribed from a gene, as well as proteins translated from such transcripts. Proteins may be naturally occurring isolated proteins or may be the product of recombinant or chemical synthesis. The term “protein fragment” refers to a protein in which amino acid residues are deleted as compared to the reference protein itself, but where the remaining amino acid sequence is usually identical to or substantially identical (for example, 100%, 99%, 95%, 90%, 85%, 80%, 75%, 70%, 65%, or 60% identical) to that of the reference protein. Such deletions may occur at the amino-terminus or carboxy-terminus of the reference protein, or alternatively both. Deletions may also occur internally.

Fragments typically are at least about 5, 6, 8 or 10 amino acids long, at least about 14 amino acids long, at least about 20, 30, 40 or 50 amino acids long, at least about 75 amino acids long, or at least about 100, 150, 200, 300, 500 or more amino acids long. Fragments may be obtained using proteinases to fragment a larger protein, or by recombinant methods, such as the expression of only part of a protein-encoding nucleotide sequence (either alone or fused with another protein-encoding nucleic acid sequence). In various embodiments, a fragment may comprise an enzymatic activity and/or an interaction site of the reference protein to, e.g., a cell receptor. In another embodiment, a fragment may have immunogenic properties. The proteins may include mutations introduced at particular loci by a variety of known techniques, which do not adversely effect, but may enhance, their use in the methods provided herein. A fragment can retain one or more of the biological activities of the reference protein.

The terms “polypeptide fragment” or “fragment”, when used in reference to a particular polypeptide, refers to a polypeptide in which amino acid residues are deleted as compared to the reference polypeptide itself, but where the remaining amino acid sequence is usually identical or substantially identical as defined herein above, to that of the reference polypeptide. Such deletions may occur at the amino-terminus or carboxy-terminus of the reference polypeptide, or alternatively both. Fragments typically are at least about 5, 6, 8 or 10 amino acids long, at least about 14 amino acids long, at least about 20, 30, 40 or 50 amino acids long, at least about 75 amino acids long, or at least about 100, 150, 200, 300, 500 or more amino acids long. A fragment can retain one or more of the biological activities of the reference polypeptide. In various embodiments, a fragment may comprise an enzymatic activity and/or an interaction site of the reference polypeptide. In another embodiment, a fragment may have immunogenic properties.

A “patient” or “subject” or “host” refers to either a human or non-human animal.

The phrase “pharmaceutically acceptable” is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.

A “pharmaceutically-acceptable carrier” as used herein means a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, or solvent encapsulating material, involved in carrying or transporting the subject compound from one organ, or portion of the body, to another organ, or portion of the body. Each carrier must be “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the patient. Some examples of materials which can serve as pharmaceutically-acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; (12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents, such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18) Ringer's solution; (19) ethyl alcohol; (20) pH buffered solutions; (21) polyesters, polycarbonates and/or polyanhydrides; and (22) other non-toxic compatible substances employed in pharmaceutical formulations.

A “pharmaceutically-acceptable salt” refers to the relatively non-toxic, inorganic and organic acid addition salts of compounds.

The term “self-assembling” as used herein refers to the ability of a heat shock protein fused to a biotin-binding protein to form a non-covalent complex with biotinylated component(s) as described herein. Such ability is conferred by the non-covalent association of biotin with a biotin-binding protein.

The term “self-assembling” as used herein refers to the ability of a heat shock protein fused to an antibody binding protein to form a non-covalent complex with an antibody or fragment thereof that binds specifically to mesothelin, as described herein. Such ability is conferred by the non-covalent association of an antibody or fragment thereof with a biotin-binding protein.

As used herein, a “stress protein,” also known as a “heat shock protein” or “Hsp,” is a protein that is encoded by a stress gene, and is therefore typically produced in significantly greater amounts upon the contact or exposure of the stressor to the organism. The term “stress protein” as used herein is intended to include such portions and peptides of a stress protein. A “stress gene,” also known as “heat shock gene”, as used herein, refers to a gene that is activated or otherwise detectably upregulated due to the contact or exposure of an organism (containing the gene) to a stressor, such as heat shock, hypoxia, glucose deprivation, heavy metal salts, inhibitors of energy metabolism and electron transport, and protein denaturants, or to certain benzoquinone ansamycins. Nover, L., Heat Shock Response, CRC Press, Inc., Boca Raton, Fla. (1991). “Stress gene” also includes homologous genes within known stress gene families, such as certain genes within the Hsp70 and Hsp90 stress gene families, even though such homologous genes are not themselves induced by a stressor. Each of the terms stress gene and stress protein as used in the present specification may be inclusive of the other, unless the context indicates otherwise.

“Treating” a disease in a subject or “treating” a subject having a disease refers to subjecting the subject to a pharmaceutical treatment, e.g., the administration of a drug, such that the extent of the disease is decreased or prevented. Treatment includes (but is not limited to) administration of a composition, such as a pharmaceutical composition, and may be performed either prophylactically, or subsequent to the initiation of a pathologic event.

The term “vaccine” refers to a substance that elicits an immune response and also confers protective immunity upon a subject.

“Vector” refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of preferred vector is an episome, i.e., a nucleic acid capable of extra-chromosomal replication. Preferred vectors are those capable of autonomous replication and/or expression of nucleic acids to which they are linked. Vectors capable of directing the expression of genes to which they are operatively linked are referred to herein as “expression vectors”. In general, expression vectors of utility in recombinant DNA techniques are often in the form of “plasmids” which refer generally to circular double stranded DNA loops, which, in their vector form are not bound to the chromosome. In the present specification, “plasmid” and “vector” are used interchangeably as the plasmid is the most commonly used form of vector. However, as will be appreciated by those skilled in the art, the invention is intended to include such other forms of expression vectors which serve equivalent functions and which become subsequently known in the art.

As used herein, “Specifically binds” means via covalent or hydrogen bonding or electrostatic attraction.

As used herein, “antibody binding protein” means any protein that can be cloned and expressed and that has affinity for any component of an antibody. For example some proteins bind to the Fc portion of the antibody while others have high affinity for the light chain (e.g. protein L). Proteins such as Protein A, Protein G, Protein A/G, Protein L. Similarly other molecules showing affinity for antibodies could be used for this purpose.

As used herein, an “immune response” or a “detectable response” includes a detectable level of a response that occurs in a subject that has been exposed to a fusion protein of the invention, as described herein, but not in a subject that has not been exposed to a fusion protein of the invention. A “response” that is detected includes but is not limited to an increase in an immune response or an increase in immunogenicity.

A “detectable response” means a response that is at least 0.01%, 0.5%, 1% or more than the response of a subject that has not been exposed to a fusion protein of the invention. A “detectable response” also means a response that is at least 0.5, 1, 2, 3, 4, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 1000-fold or more greater than the response of a subject that has not been exposed to a fusion protein of the invention.

As used herein, “immunogenicity” refers to the ability, for example the ability of a fusion protein of the invention to induce humoral and/or cell-mediated immune responses.

As used herein, “immune response” refers to a response made by the immune system of an organism to a substance, which includes but is not limited to foreign or self proteins. There are three general types of “immune response” including, but not limited to mucosal, humoral and cellular “immune responses.” A “mucosal immune response” results from the production of secretory IgA (sIgA) antibodies in secretions that bathe all mucosal surfaces of the respiratory tract, gastrointestinal tract and the genitourinary tract and in secretions from all secretory glands (McGhee, J. R. et al., 1983, Annals NY Acad. Sci. 409). These sIgA antibodies act to prevent colonization of pathogens on a mucosal surface (Williams, R. C. et al., Science 177, 697 (1972); McNabb, P. C. et al., Ann. Rev. Microbiol. 35, 477 (1981)) and thus act as a first line of defense to prevent colonization or invasion through a mucosal surface. The production of sIgA can be stimulated either by local immunization of the secretory gland or tissue or by presentation of an antigen to either the gut-associated lymphoid tissue (GALT or Peyer's patches) or the bronchial-associated lymphoid tissue (BALT; Cebra, J. J. et al., Cold Spring Harbor Symp. Quant. Biol. 41, 210 (1976); Bienenstock, J. M., Adv. Exp. Med. Biol. 107, 53 (1978); Weisz-Carrington, P. et al., J. Immunol. 123, 1705 (1979); McCaughan, G. et al., Internal Rev. Physiol 28, 131 (1983)). Membranous microfold cells, otherwise known as M cells, cover the surface of the GALT and BALT and may be associated with other secretory mucosal surfaces. M cells act to sample antigens from the luminal space adjacent to the mucosal surface and transfer such antigens to antigen-presenting cells (dendritic cells and macrophages), which in turn present the antigen to a T lymphocyte (in the case of T-dependent antigens), which process the antigen for presentation to a committed B cell. B cells are then stimulated to proliferate, migrate and ultimately be transformed into an antibody-secreting plasma cell producing IgA against the presented antigen. When the antigen is taken up by M cells overlying the GALT and BALT, a generalized mucosal immunity results with sIgA against the antigen being produced by all secretory tissues in the body (Cebra et al., supra; Bienenstock et al., supra; Weinz-Carrington et al., supra; McCaughan et al., supra). Oral immunization is therefore an important route to stimulate a generalized mucosal immune response and, in addition, leads to local stimulation of a secretory immune response in the oral cavity and in the gastrointestinal tract.

An “immune response” may be measured using techniques known to those of skill in the art. For example, serum, blood or other secretions may be obtained from an organism for which an “immune response” is suspected to be present, and assayed for the presence of the above mentioned immunoglobulins using an enzyme-linked immuno-absorbant assay (ELISA; U.S. Pat. No. 5,951,988; Ausubel et al., Short Protocols in Molecular Biology 3^(rd) Ed. John Wiley & Sons, Inc. 1995). A statistical test known in the art may be used to determine the difference in measured immunoglobulin levels including, but not limited to ANOVA, Student's T-test, and the like, wherein the P value is at least <0.1, <0.05, <0.01, <0.005, <0.001, and even <0.0001.

An “immune response” may be measured using other techniques such as immunohistochemistry using labeled antibodies which are specific for portions of the immunoglobulins raised during the “immune response”. Microscopic data obtained by immunohistochemistry may be quantitated by scanning the immunohistochemically stained tissue sample and quantitating the level of staining using a computer software program known to those of skill in the art including, but not limited to NIH Image (National Institutes of Health, Bethesda, Md.). According to the present invention, a fusion protein of the present invention can be said to stimulate an “immune response” if the quantitative measure of immunohistochemical staining in a subject treated with a fusion protein is statistically different from the measure of immunohistochemical staining detected in a subject not treated with a fusion protein. A statistical test known in the art may be used to determine the difference in measured immunohistochemical staining levels including, but not limited to ANOVA, Student's T-test, and the like, wherein the P value is at least <0.1, <0.05, <0.01, <0.005, <0.001, and even <0.0001.

1. Engineered Fusion Proteins

Provided are fusion proteins comprising: a stress protein fused to an engineered antibody or fragment thereof, that binds specifically to mesothelin; a stress protein fused to a biotin-binding protein, a stress protein fused to an antibody binding protein, an engineered antibody that binds specifically to mesothelin fused to a biotin binding protein and an engineered antibody that binds specifically to mesothelin fused to an antibody binding protein (see FIGS. 1-19).

The engineered mesothelin antibody may comprise for example, at least one scFv, at least one Fab fragment, at least one Fv fragment, etc. It may be monovalent or it may be multivalent. In embodiments wherein the engineered antibody is multivalent, it may be bivalent, trivalent, tetravalent, etc. The multivalent antibodies may be monospecific or multispecific, e.g., bispecific, trispecific, tetraspecific, etc. The multivalent antibodies may be in any form, such as a diabody, triabody, tetrabody, etc. In certain embodiments, the engineered antibody is a Tandab. The stress protein may comprise any stress protein. In certain embodiments, the stress protein comprises HSP70, for example, Mycobacterium tuberculosis HSP70 or Mycobacterium bovis HSP70. The full-length polypeptide sequences of Mycobacterium tuberculosis HSP70 and Mycobacterium bovis HSP70 are depicted in FIGS. 20A and 20B, respectively.

Further detail about engineered antibodies, stress proteins, biotin-binding proteins and antibody binding proteins which may be incorporated into the subject fusion polypeptides is provided below.

A. Engineered Antibodies

Natural antibodies are themselves dimers, and thus, bivalent. If two hybridoma cells producing different antibodies are artificially fused, some of the antibodies produced by the hybrid hybridoma are composed of two monomers with different specificities. Such bispecific antibodies can also be produced by chemically conjugating two antibodies. Natural antibodies and their bispecific derivatives are relatively large and expensive to produce. The constant domains of mouse antibodies are also a major cause of the human anti-mouse antibody (HAMA) response, which prevents their extensive use as therapeutic agents. They can also give rise to unwanted effects due to their binding of Fc-receptors. For these reasons, molecular immunologists have been concentrating on the production of the much smaller Fab- and Fv-fragments in microorganisms. These smaller fragments are not only much easier to produce, they are also less immunogenic, have no effector functions, and, because of their relatively small size, they are better able to penetrate tissues and tumors. In the case of the Fab-fragments, the constant domains adjacent to the variable domains play a major role in stabilizing the heavy and light chain dimer. Accordingly, while full-length or nearly full length engineered antibodies may comprise the subject fusion polypeptides, smaller, single domain engineered antibodies (that may be multivalent and multispecific) are preferred for use in the fusion polypeptides.

The Fv-fragment is much less stable, and a peptide linker may therefore be introduced between the heavy and light chain variable domains to increase stability. This construct is known as a single chain Fv(scFv)-fragment. A disulfide bond is sometimes introduced between the two domains for extra stability. Thus far, tetravalent scFv-based antibodies have been produced by fusion to extra polymerizing domains such as the streptavidin monomer that forms tetramers, and to amphipathic alpha helices. However, these extra domains can increase the immunogenicity of the tetravalent molecule.

Bivalent and bispecific antibodies can be constructed using only antibody variable domains. A fairly efficient and relatively simple method is to make the linker sequence between the V_(H) and V_(L) domains so short that they cannot fold over and bind one another. Reduction of the linker length to 3-12 residues prevents the monomeric configuration of the scFv molecule and favors intermolecular V_(H)-V_(L) pairings with formation of a 60 kDa non-covalent scFv dimer “diabody” (Holliger et al., 1993, Proc. Natl. Acad. Sci. USA 90, 6444-6448). The diabody format can also be used for generation of recombinant bispecific antibodies, which are obtained by the noncovalent association of two single-chain fusion products, consisting of the V_(H) domain from one antibody connected by a short linker to the V_(L) domain of another antibody. Reducing the linker length still further below three residues can result in the formation of trimers (“triabody”, about 90 kDa) or tetramers (“tetrabody”, about 120 kDa) (Le Gall et al., 1999, FEBS Letters 453, 164-168). For a review of engineered antibodies, particularly single domain fragments, see Holliger and Hudson, 2005, Nature Biotechnology, 23:1126-1136. All of such engineered antibodies may be used in the fusion polypeptides provided herein.

Other multivalent engineered antibodies that may comprise the subject fusion polypeptides are described in Lu, et al., 2003, J. Immunol. Meth. 279:219-232 (di-diabodies or tetravalent bispecific antibodies); US Published Application 20050079170 (multimeric Fv molecules or “flexibodies”), and WO99/57150 and Kipriyanov, et al., 1999, J. Mol. Biol. 293:41-56 (tandem diabodies, or “Tandabs”).

Any of the above-described multivalent engineered antibodies may be developed by one of skill in the art using routine recombinant DNA techniques, for example as described in PCT International Application No. PCT/US86/02269; European Patent Application No. 184,187; European Patent Application No. 171,496; European Patent Application No. 173,494; PCT International Publication No. WO 86/01533; U.S. Pat. No. 4,816,567; European Patent Application No. 125,023; Better et al. (1988)Science 240:1041-1043; Liu et al. (1987) Proc. Natl. Acad. Sci. USA 84:3439-3443; Liu et al. (1987) J. Immunol. 139:3521-3526; Sun et al. (1987) Proc. Natl. Acad. Sci. USA 84:214-218; Nishimura et al. (1987) Cancer Res. 47:999-1005; Wood et al. (1985) Nature 314:446-449; Shaw et al. (1988) J. Natl. Cancer Inst. 80:1553-1559); Morrison (1985) Science 229:1202-1207; Oi et al. (1986) BioTechniques 4:214; U.S. Pat. No. 5,225,539; Jones et al. (1986) Nature 321:552-525; Verhoeyan et al. (1988) Science 239:1534; Beidler et al. (1988) J. Immunol. 141:4053-4060; and Winter and Milstein, Nature, 349, pp. 293-99 (1991)). Preferably non-human antibodies are “humanized” by linking the non-human antigen binding domain with a human constant domain (e.g. Cabilly et al., U.S. Pat. No. 4,816,567; Morrison et al., Proc. Natl. Acad. Sci. U.S.A., 81, pp. 6851-55 (1984)).

The antigen recognition sites or entire variable regions of the engineered antibodies may be derived from one or more parental antibodies directed against mesothelin. The parental antibodies can include naturally occurring antibodies or antibody fragments, antibodies or antibody fragments adapted from naturally occurring antibodies, antibodies constructed de novo using sequences of antibodies or antibody fragments known to be specific for an antigen of interest. Sequences that may be derived from parental antibodies include heavy and/or light chain variable regions and/or CDRs, framework regions or other portions thereof.

Multivalent, multispecific antibodies may contain a heavy chain comprising two or more variable regions and/or a light chain comprising one or more variable regions wherein at least two of the variable regions recognize different epitopes on the same antigen.

Candidate engineered antibodies for inclusion in the fusion polypeptides, or the fusion polypeptides themselves, may be screened for activity using a variety of known assays. For example, screening assays to determine binding specificity are well known and routinely practiced in the art. For a comprehensive discussion of such assays, see Harlow et al. (Eds.), ANTIBODIES: A LABORATORY MANUAL; Cold Spring Harbor Laboratory; Cold Spring Harbor, N.Y., 1988, Chapter 6.

B. Stress Proteins

Any suitable stress protein (heat shock protein (hsp)) can be used in the fusion polypeptides of the present invention.

A “heat shock protein” is encoded by a “heat shock gene” or a stress gene, refers to the protein product of a gene that is activated or otherwise detectably upregulated due to the contact or exposure of an organism (containing the gene) to a stressor, such as heat shock, hypoxia, glucose deprivation, heavy metal salts, inhibitors of energy metabolism and electron transport, and protein denaturants, or to certain benzoquinone ansamycins. Nover, L., Heat Shock Response, CRC Press, Inc., Boca Raton, Fla. (1991). “Heat shock protein” also includes homologous proteins encoded by genes within known stress gene families, even though such homologous genes are not themselves induced by a stressor. A “heat shock protein fusion” refers to a heat shock protein or portion thereof, linked to at least one of an engineered mesothelin antibody, a biotin binding protein or an antibody binding protein.

Cells respond to a stressor (typically heat shock treatment) by increasing the expression of a group of genes commonly referred to as stress, or heat shock genes. Heat shock treatment involves exposure of cells or organisms to temperatures that are one to several degrees Celsius above the temperature to which the cells are adapted. In coordination with the induction of such genes, the levels of corresponding stress proteins increase in stressed cells.

For example, a heat shock protein may be C- or N-terminally joined to a biotin-binding protein, an antibody binding protein or a mesothelin antibody to generate a heat shock protein fusion. When administered in conjunction with a biotinylated component provided herein, a heat shock protein fusion comprising a heat shock protein and a biotin binding protein is capable of stimulating humoral and/or cellular immune responses, including CD8 cytotoxic T cell (CTL) responses, to an antigen of interest.

For example, but not by way of limitation, heat shock proteins which may be used according to the invention include BiP (also referred to as grp78), Hsp10, Hsp20-30, Hsp60 hsp70, hsc70, gp96 (grp94), hsp60, hsp40, and Hsp100-200, Hsp100, Hsp90, and members of the families thereof. Especially preferred heat shock proteins are BiP, gp96, and hsp70, as exemplified below. A particular group of heat shock proteins includes Hsp90, Hsp70, Hsp60, Hsp20-30, further preferably Hsp70 and Hsp60. Most preferred is a member of the hsp70 family.

In bacteria, the predominant stress proteins are proteins with molecular sizes of about 70 and 60 kDa, respectively, that are commonly referred to as Hsp70 and Hsp60, respectively. These and other specific stress proteins and the genes encoding them are discussed further below. In bacteria, Hsp70 and Hsp60 typically represent about 1-3% of cell protein based on the staining pattern using sodium dodecyl sulfate polyacrylamide gel electrophoresis and the stain Coomassie blue, but accumulate to levels as high as 25% under stressful conditions. Stress proteins appear to participate in important cellular processes such as protein synthesis, intracellular trafficking, and assembly and disassembly of protein complexes. It appears that the increased amounts of stress proteins synthesized during stress serve primarily to minimize the consequences of induced protein unfolding. Indeed, the preexposure of cells to mildly stressful conditions that induce the synthesis of stress proteins affords protection to the cells from the deleterious effects of a subsequent more extreme stress.

The major stress proteins appear to be expressed in every organism and tissue type examined so far. Also, it appears that stress proteins represent the most highly conserved group of proteins identified to date. For example, when stress proteins in widely diverse organisms are compared, Hsp90 and Hsp70 exhibit 50% or higher identity at the amino acid level and share many similarities at non-identical positions. It is noted that similar or higher levels of homology exist between different members of a particular stress protein family within species.

The stress proteins, particularly Hsp70, Hsp60, Hsp20-30 and Hsp 10, are among the major determinants recognized by the host immune system in the immune response to infection by Mycobacterium tuberculosis and Mycobacterium leprae. Young, R. A. and Elliott. T. J., Stress Proteins, Infection, And Immune Surveillance, Cell 50:5-8 (1989). Further, some rat arthritogenic T cells recognize Hsp60 epitopes. Van Eden, W. et al., Nature 331:171-173 (1988). However, individuals, including healthy individuals, with no history of mycobacterial infection or autoimmune disease also carry T cells that recognize both bacterial and human Hsp60 epitopes; a considerable fraction of T cells in healthy individuals that are characterized by expression of the gamma-delta T cell receptor recognize both self and foreign stress proteins. O'Brien, R. et al., Cell 57:664-674 (1989). Thus, individuals, even healthy individuals, possess T-cell populations that recognize both foreign and self stress protein epitopes.

This system recognizing stress protein epitopes presumably constitutes an “early defense system” against invading organisms. Murray, P. J. and Young, R. A., J. Bacteriol 174: 4193-6 (1992). The system may be maintained by frequent stimulation by bacteria and viruses. As discussed before, healthy individuals have T cell populations recognizing self stress proteins. Thus, the presence of autoreactive T cells is compatible with normal health and does not cause autoimmune disease; this demonstrates the safety of stress proteins within an individual. The safety of stress proteins is additionally demonstrated by the success and relative safety of BCG (Bacille Calmette Guerin, a strain of Mycobacterium bovis) vaccinations, which induce an immune response against stress proteins that is also protective against Mycobacterium tuberculosis.

Families of stress genes and proteins for use in the fusion polypeptides are those well known in the art and include, for example, Hsp 100-200, Hsp100, Hsp90, Lon, Hsp70, Hsp60, TF55, Hsp40, FKBPs, cyclophilins, Hsp20-30, ClpP, GrpE, Hsp10, ubiquitin, calnexin, and protein disulfide isomerases. Macario, A. J. L., Cold Spring Harbor Laboratory Res. 25:59-70, 1995; Parsell, D. A. & Lindquist, S. Ann. Rev. Genet. 27:437-496 (1993); U.S. Pat. No. 5,232,833 (Sanders et al.). A particular group of stress proteins includes Hsp90, Hsp70. Hsp60, Hsp20-30, further preferably Hsp70 and Hsp60.

Hsp100 examples include mammalian Hsp110, yeast Hsp104, ClpA, ClpB, ClpC, ClpX and ClpY. Yeast Hsp104 and E. coli ClpA, form hexameric and E. coli ClpB, tetrameric particles whose assembly appears to require adenine nucleotide binding. Clp protease provides a 750 kDa heterooligomer composed of ClpP (a proteolytic subunit) and of ClpA. ClpB-Y are structurally related to ClpA, although unlike ClpA they do not appear to complex with ClpP.

Hsp90 examples include HtpG in E. coli, Hsp83 and Hsc83 yeast, and Hsp90alpha, Hsp90beta and Grp94 in humans. Hsp90 binds groups of proteins, which proteins are typically cellular regulatory molecules such as steroid hormone receptors (e.g., glucocorticoid, estrogen, progesterone, and testosterone receptors), transcription factors and protein kinases that play a role in signal transduction mechanisms. Hsp90 proteins also participate in the formation of large, abundant protein complexes that include other stress proteins.

Lon is a tetrameric protein functioning as an ATP-dependent protease degrading non-native proteins in E. coli.

Hsp70 examples include Hsp72 and Hsc73 from mammalian cells, DnaK from bacteria, particularly mycobacteria such as Mycobacterium leprae, Mycobacterium tuberculosis, and Mycobacterium bovis (such as Bacille-Calmette Guerin: referred to herein as Hsp71), DnaK from Escherichia coli, yeast, and other prokaryotes, and BiP and Grp78. Hsp70 is capable of specifically binding ATP as well as unfolded polypeptides and peptides, thereby participating in protein folding and unfolding as well as in the assembly and disassembly of protein complexes.

Hsp60 examples include Hsp65 from mycobacteria. Bacterial Hsp60 is also commonly known as GroEL, such as the GroEL from E. coli. Hsp60 forms large homooligomeric complexes, and appears to play a key role in protein folding. Hsp60 homologues are present in eukaryotic mitochondria and chloroplasts.

TF55 examples include Tcpl, TRiC and thermosome. The proteins typically occur in the cytoplasm of eukaryotes and some archaebacteria, and form multi-membered rings, promoting protein folding. They are also weakly homologous to Hsp60.

Hsp40 examples include DnaJ from prokaryotes such as E. coli and mycobacteria and HSJ1, HDJ1 and Hsp40. Hsp40 plays a role as a molecular chaperone in protein folding, thermotolerance and DNA replication, among other cellular activities.

FKBPs examples include FKBP12, FKBP13, FKBP25, and FKBP59, Fprl and Nepl. The proteins typically have peptidyl-prolyl isomerase activity and interact with immunosuppressants such as FK506 and rapamycin. The proteins are typically found in the cytoplasm and the endoplasmic reticululum.

Cyclophilin examples include cyclophilins A, B and C. The proteins have peptidyl-prolyl isomerase activity and interact with the immunosuppressant cyclosporin A. The protein cyclosporin A binds calcineurin (a protein phosphatase).

Hsp20-30 is also referred to as small Hsp. Hsp20-30 is typically found in large homooligomeric complexes or, possibly, also heterooligomeric complexes where an organism or cell type expresses several different types of small Hsps. Hsp20-30 interacts with cytoskeletal structures, and may play a regulatory role in the polymerization/depolymerization of actin. Hsp20-30 is rapidly phosphorylated upon stress or exposure of resting cells to growth factors. Hsp20-30 homologues include alpha-crystallin.

ClpP is an E. coli protease involved in degradation of abnormal proteins. Homologues of ClpP are found in chloroplasts. ClpP forms a heterooligomeric complex with ClpA.

GrpE is an E. coli protein of about 20 kDa that is involved in both the rescue of stress-damaged proteins as well as the degradation of damaged proteins. GrpE plays a role in the regulation of stress gene expression in E. coli.

Hsp10 examples include GroES and Cpn10. Hsp10 is typically found in E. coli and in mitochondria and chloroplasts of eukaryotic cells. Hsp10 forms a seven-membered ring that associates with Hsp60 oligomers. Hsp10 is also involved in protein folding.

Ubiquitin has been found to bind proteins in coordination with the proteolytic removal of the proteins by ATP-dependent cytosolic proteases.

In particular embodiments, the stress proteins of the present invention are obtained from enterobacteria, mycobacteria (particularly M leprae, M. tuberculosis, M. vaccae, M. smegmatis and M. bovis), E. coli, yeast, Drosophila, vertebrates, avians, chickens, mammals, rats, mice, primates, or humans.

Naturally occurring or recombinantly derived mutants of heat shock proteins may be used according to the invention. For example, but not by way of limitation, the present invention provides for the use of heat shock proteins mutated so as to facilitate their secretion from the cell (for example having mutation or deletion of an element which facilitates endoplasmic reticulum recapture, such as KDEL (SEQ ID NO: 4) or its homologues; such mutants are described in PCT Application No. PCT/US96/13233 (WO 97/06685), which is incorporated herein by reference.

In particular embodiments, e.g., in cases involving chemical conjugates between a stress protein and an engineered mesothelin antibody, the stress proteins used are isolated stress proteins, which means that the stress proteins have been selected and separated from the host cell in which they were produced. Such isolation can be carried out as described herein and using routine methods of protein isolation known in the art.

The stress proteins may be in the form of acidic or basic salts, or in neutral form. In addition, individual amino acid residues may be modified by oxidation or reduction. Furthermore, various substitutions, deletions, or additions may be made to the amino acid or nucleic acid sequences, the net effect of which is to retain or further enhance the increased biological activity of the stress protein. Due to code degeneracy, for example, there may be considerable variation in nucleotide sequences encoding the same amino acid sequence. Portions of stress proteins or peptides obtained from stress proteins may be used in the fusion polypeptides, provided such portions or peptides include the epitopes involved with enhancing the immune response. Portions of stress proteins may be obtained by fragmentation using proteinases, or by recombinant methods, such as the expression of only part of a stress protein-encoding nucleotide sequence (either alone or fused with another protein-encoding nucleic acid sequence). Peptides may also be produced by such methods, or by chemical synthesis. The stress proteins may include mutations introduced at particular loci by a variety of known techniques. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual. 2d Ed., Cold Spring Harbor Laboratory Press (1989); Drinkwater and Klinedinst Proc. Natl. Acad. Sci. USA 83:3402-3406 (1986); Liao and Wise, Gene 88:107-111 (1990): Horwitz et al., Genome 3:112-117 (1989).

The pharmaceutical compositions provided herein may have individual amino acid residues that are modified by oxidation or reduction. Furthermore, various substitutions, deletions, or additions may be made to the amino acid or nucleic acid sequences, the net effect of which is to retain or further enhance the increased biological activity of the heat shock protein. Due to codon degeneracy, for example, there may be considerable variation in nucleotide sequences encoding the same amino acid sequence.

The term “heat shock protein” is intended to encompass fragments of heat shock proteins obtained from heat shock proteins, provided such fragments include the epitopes involved with enhancing the immune response to mesothelin. Fragments of heat shock proteins may be obtained using proteinases, or by recombinant methods, such as the expression of only part of a stress protein-encoding nucleotide sequence (either alone or fused with another protein-encoding nucleic acid sequence). The heat shock proteins may include mutations introduced at particular loci by a variety of known techniques to enhance its effect on the immune system. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, 2d Ed., Cold Spring Harbor Laboratory Press (1989); Drinkwater and Klinedinst Proc. Natl. Acad. Sci. USA 83:3402-3406 (1986); Liao and Wise, Gene 88:107-111 (1990); Horwitz et al., Genome 3:112-117 (1989).

In particular embodiments, the heat shock proteins used in the present invention are isolated heat shock proteins, which means that the heat shock proteins have been selected and separated from the host cell in which they were produced. Such isolation can be carried out as described herein and using routine methods of protein isolation known in the art. Maniatis et al., Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1982); Sambrook et al., Molecular Cloning: A Laboratory Manual, 2d Ed., Cold Spring Harbor Laboratory Press (1989); Deutscher, M., Guide to Protein Purification Methods Enzymology, vol. 182, Academic Press, Inc., San Diego, Calif. (1990).

C. Biotin Binding Proteins

The invention provides for biotin binding proteins including but not limited to avidin, streptavidin, or neutravidin. Any naturally occurring or engineered biotin binding protein known in the art is useful according to the invention.

A pH-sensitive mutant of avidin, streptavidin, or neutravidin, for example, may be employed to control the noncovalent interaction of avidin-, streptavidin-, or neutravidin-to biotin, and thereby achieve the desired stoichiometry of heat shock protein fusion with the various permutations and combinations of biotinylated component, as described herein. The choice of wild-type or a particular mutant form of biotin-binding protein such as avidin may be employed to control the desired valency of the pharmaceutical composition (e.g., monomeric, dimeric, or tetrameric form of avidin). Monovalent or divalent vaccines may be similarly produced by employing heat shock fusion proteins comprising other avidin, streptavidin, or neutravidin mutant proteins that bind biotin but in a monovalent or divalent fashion. An example of an avidin mutant is monomeric avidin.

An example of a pH-sensitive point mutant of Avidin which confers pH-adjustable biotin binding is Y33H. Another mutant has substitutions of histidine for Met96, Val115, and Ile117, optionally with histidine replacement at Trp110. Such approaches for controlling biotin-streptavidin binding are described in Laitinen, O. H. (2007), “Brave (Strept)avidins in Biotechnology,” Trends in Biotechnology 25 (6): 269-277 and Nordlund, H. R. (2003), “Introduction of histidine residues into avidin subunit interfaces allows pH-dependent regulation of quaternary structure and biotin binding,” FEBS Letters 555: 449-454, the contents of both of which are incorporated herein by reference.

D. Antibody Binding Proteins

An antibody binding protein useful according to the invention includes but is not limited to Protein A, Protein G, Protein A/G, and Protein L. Protein A binds the heavy chain Fc portion of immunoglobulins. An antibody binding protein binds with high affinity to human IgG1 and IgG2 as well as mouse IgG2a and IgG2b. Protein G, like Protein A binds immunoglobulins through the Fc portion of the heavy chain. Native Protein G naturally binds serum albumin. Recombinant Protein G has been engineered not to bind serum albumin. Protein L binds immunoglobulins through the kappa light chain. It binds a broader range of antibodies since it does not rely on the Fc portion of the heavy chain. However, protein L binds human VκI, VκIII and VκIV subtypes but does not bind the VκII subtype. In mouse, it only binds antibodies having the VκI light chain.

E. Biotinylated Components

The term “biotinylated component” as used herein, refers to a biotinylated protein. Non-limiting examples of biotinylated proteins include biotinylated antigens, antibodies, and costimulatory molecules. The biotinylated component is to be administered to a subject in conjunction with a heat shock protein fusion as described herein. For example, in one embodiment a fusion protein comprising a stress protein fused to a biotin-binding protein is used in combination with a biotinylated antibody that binds specifically to mesothelin.

In one embodiment, an antibody or fragment thereof, that binds specifically to mesothelin may be biotinylated and administered in conjunction with a heat shock protein fusion comprising a heat shock fusion fused with a biotin binding protein, as described herein.

2. Methods of Making the Fusion Proteins

Provided also are compositions and methods for making fusion proteins according to the invention. Any of the fusion proteins described herein can be produced by recombinant means. For example, a nucleic acid encoding a stress protein can be joined to either end of a nucleic acid sequence encoding an engineered mesothelin antibody or fragment thereof, the antibody binding protein or the biotin binding protein, or combinations thereof, such that the protein-coding sequences are sharing a common translational reading frame and can be expressed as a fusion protein including, for example, the engineered mesothelin antibody or fragment thereof, and the stress protein.

The combined sequence is inserted into a suitable vector chosen based on the expression features desired and the nature of the host cell. In the examples provided hereinafter, the nucleic acid sequences are assembled in a vector suitable for protein expression in the bacterium E. coli. Following expression in the chosen host cell, fusion protein can be purified by routine biochemical separation techniques or by immunoaffinity methods using an antibody to one of the components of the fusion protein. Alternatively, the selected vector can add a tag to the fusion protein sequence, e.g., an oligohistidine tag, permitting expression of a tagged fusion protein that can be purified by affinity methods using an antibody or other material having an appropriately high affinity for the tag. Sambrook et al., Molecular Cloning: A Laboratory Manual, 2d Ed., Cold Spring Harbor Laboratory Press (1989); Deutscher, M. Guide to Protein Purification Methods Enzymology, vol. 182. Academic Press, Inc. San Diego, Calif. (1990). If a vector suitable for expression in mammalian cells is used. e.g., one of the vectors discussed below, the fusion protein can be expressed and purified from mammalian cells. Alternatively, the mammalian expression vector (including fusion protein-coding sequences) can be administered to a subject to direct expression of a fusion protein according to the method of the invention in the subject's cells. A nucleic acid encoding fusion protein of the invention can also be produced chemically and then inserted into a suitable vector for fusion protein production and purification or administration to a subject. Finally, a fusion protein can also be prepared chemically.

Techniques for making fusion genes are well known in the art. Essentially, the joining of various DNA fragments coding for different polypeptide sequences is performed in accordance with conventional techniques, employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene may be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments may be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which may subsequently be annealed to generate a chimeric gene sequence (see, for example, Current Protocols in Molecular Biology, eds. Ausubel et al., John Wiley & Sons: 1992). Accordingly, provided is an isolated nucleic acid comprising a fusion gene of a gene encoding at least one engineered antibody and a gene encoding at least one stress protein.

The nucleic acid may be provided in a vector comprising a nucleotide sequence encoding an engineered fusion protein according to the invention, and operably linked to at least one regulatory sequence. It should be understood that the design of the expression vector may depend on such factors as the choice of the host cell to be transformed and/or the type of protein desired to be expressed. The vector's copy number, the ability to control that copy number and the expression of any other protein encoded by the vector, such as antibiotic markers, should be considered. Such vectors may be administered in any biologically effective carrier, e.g., any formulation or composition capable of effectively transfecting cells either ex vivo or in vivo with genetic material encoding a chimeric polypeptide. Approaches include insertion of the nucleic acid into viral vectors including recombinant retroviruses, adenoviruses, adeno-associated viruses, human immunodeficiency viruses, and herpes simplex viruses-1, or recombinant bacterial or eukaryotic plasmids. Viral vectors may be used to transfect cells directly; plasmid DNA may be delivered alone with the help of, for example, cationic liposomes (lipofectin) or derivatized (e.g., antibody conjugated), polylysine conjugates, gramicidin S, artificial viral envelopes or other such intracellular carriers. Nucleic acids may also be directly injected. Alternatively, calcium phosphate precipitation may be carried out to facilitate entry of a nucleic acid into a cell.

The subject nucleic acids may be used to cause expression and over-expression of a fusion protein of the invention in cells propagated in culture, e.g. to produce fusion proteins or polypeptides.

Provided also is a host cell transfected with a recombinant gene in order to express an engineered mesothelin antibody fusion protein. The host cell may be any prokaryotic or eukaryotic cell. For example, a stress protein fusion may be expressed in bacterial cells, such as E. coli, insect cells (baculovirus), yeast, insect, plant, or mammalian cells. In those instances when the host cell is human, it may or may not be in a live subject. Other suitable host cells are known to those skilled in the art. Additionally, the host cell may be supplemented with tRNA molecules not typically found in the host so as to optimize expression of the polypeptide. Other methods suitable for maximizing expression of the fusion polypeptide will be known to those in the art.

A cell culture includes host cells, media and other byproducts. Suitable media for cell culture are well known in the art. A fusion polypeptide may be secreted and isolated from a mixture of cells and medium comprising the polypeptide. Alternatively, a fusion polypeptide may be retained cytoplasmically and the cells harvested, lysed and the protein isolated. A fusion polypeptide may be isolated from cell culture medium, host cells, or both using techniques known in the art for purifying proteins, including ion-exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, and immunoaffinity purification with antibodies specific for particular epitopes of a fusion.

Thus, a nucleotide sequence encoding all or part of a fusion protein of the invention may be used to produce a recombinant form of a protein via microbial or eukaryotic cellular processes. Ligating the sequence into a polynucleotide construct, such as an expression vector, and transforming or transfecting into hosts, either eukaryotic (yeast, avian, insect or mammalian) or prokaryotic (bacterial cells), are standard procedures. Similar procedures, or modifications thereof, may be employed to prepare recombinant fusion polypeptides by microbial means or tissue-culture technology in accord with the subject invention.

Expression vehicles for production of a recombinant protein include plasmids and other vectors. For instance, suitable vectors for the expression of a fusion polypeptide include plasmids of the types: pBR322-derived plasmids, pEMBL-derived plasmids, pEX-derived plasmids, pBTac-derived plasmids and pUC-derived plasmids for expression in prokaryotic cells, such as E. coli.

In another embodiment, the nucleic acid is a fusion protein operably linked to a bacterial promoter, e.g., the anaerobic E. coli, NirB promoter or the E. coli lipoprotein IIp promoter, described, e.g., in Inouye et al. (1985) Nucl. Acids Res. 13:3101; Salmonella pagC promoter (Miller et al., supra), Shigella ent promoter (Schmitt and Payne, J. Bacteriol. 173:816 (1991)), the tet promoter on Tn10 (Miller et al., supra), or the ctx promoter of Vibrio cholera. Any other promoter can be used. The bacterial promoter can be a constitutive promoter or an inducible promoter. An exemplary inducible promoter is a promoter which is inducible by iron or in iron-limiting conditions. In fact, some bacteria, e.g., intracellular organisms, are believed to encounter iron-limiting conditions in the host cytoplasm. Examples of iron-regulated promoters of FepA and TonB are known in the art and are described, e.g., in the following references: Headley, V. et al. (1997) Infection & Immunity 65:818; Ochsner, U. A. et al. (1995) Journal of Bacteriology 177:7194; Hunt, M. D. et al. (1994) Journal of Bacteriology 176:3944; Svinarich, D. M. and S. Palchaudhuri. (1992) Journal of Diarrhoeal Diseases Research 10:139; Prince, R. W. et al. (1991) Molecular Microbiology 5:2823; Goldberg, M. B. et al. (1990) Journal of Bacteriology 172:6863; de Lorenzo, V. et al. (1987) Journal of Bacteriology 169:2624; and Hantke, K. (1981) Molecular & General Genetics 182:288.

A plasmid preferably comprises sequences required for appropriate transcription of the nucleic acid in bacteria, e.g., a transcription termination signal. The vector can further comprise sequences encoding factors allowing for the selection of bacteria comprising the nucleic acid of interest, e.g., gene encoding a protein providing resistance to an antibiotic, sequences required for the amplification of the nucleic acid, e.g., a bacterial origin of replication.

In another embodiment, a signal peptide sequence is added to the construct, such that the fusion protein/polypeptide is secreted from cells. Such signal peptides are well known in the art.

In one embodiment, the powerful phage T5 promoter, that is recognized by E. coli RNA polymerase is used together with a lac operator repression module to provide tightly regulated, high level expression or recombinant proteins in E. coli. In this system, protein expression is blocked in the presence of high levels of lac repressor. In one embodiment, the DNA is operably linked to a first promoter and the bacterium further comprises a second DNA encoding a first polymerase which is capable of mediating transcription from the first promoter, wherein the DNA encoding the first polymerase is operably linked to a second promoter. In a preferred embodiment, the second promoter is a bacterial promoter, such as those delineated above. In an even more preferred embodiment, the polymerase is a bacteriophage polymerase, e.g., SP6, T3, or T7 polymerase and the first promoter is a bacteriophage promoter, e.g., an SP6, T3, or T7 promoter, respectively. Plasmids comprising bacteriophage promoters and plasmids encoding bacteriophage polymerases can be obtained commercially, e.g., from Promega Corp. (Madison, Wis.) and InVitrogen (San Diego, Calif.), or can be obtained directly from the bacteriophage using standard recombinant DNA techniques (J. Sambrook, E. Fritsch, T. Maniatis, Molecular Cloning: A Laboratory Manual, Cold Spring Laboratory Press, 1989). Bacteriophage polymerases and promoters are further described, e.g., in the following references: Sagawa, H. et al. (1996) Gene 168:37; Cheng, X. et al. (1994) PNAS USA 91:4034; Dubendorff, J. W. and F. W. Studier (1991) Journal of Molecular Biology 219:45; Bujarski, J. J. and P. Kaesberg (1987) Nucleic Acids Research 15:1337; and Studier, F. W. et al. (1990) Methods in Enzymology 185:60). Such plasmids can be modified further according to the specific embodiment of the fusion polypeptide to be expressed.

In another embodiment, the bacterium further comprises a DNA encoding a second polymerase which is capable of mediating transcription from the second promoter, wherein the DNA encoding the second polymerase is operably linked to a third promoter. The third promoter may be a bacterial promoter. However, more than two different polymerases and promoters could be introduced in a bacterium to obtain high levels of transcription. The use of one or more polymerases for mediating transcription in the bacterium can provide a significant increase in the amount of polypeptide in the bacterium relative to a bacterium in which the DNA is directly under the control of a bacterial promoter. The selection of the system to adopt will vary depending on the specific use, e.g., on the amount of protein that one desires to produce.

Generally, a nucleic acid encoding a fusion protein of the invention is introduced into a host cell, such as by transfection, and the host cell is cultured under conditions allowing expression of the fusion polypeptide. Methods of introducing nucleic acids into prokaryotic and eukaryotic cells are well known in the art. Suitable media for mammalian and prokaryotic host cell culture are well known in the art. Generally, the nucleic acid encoding the subject fusion polypeptide is under the control of an inducible promoter, which is induced once the host cells comprising the nucleic acid have divided a certain number of times. For example, where a nucleic acid is under the control of a beta-galactose operator and repressor, isopropyl beta-D-thiogalactopyranoside (IPTG) is added to the culture when the bacterial host cells have attained a density of about OD₆₀₀ 0.45-0.60. The culture is then grown for some more time to give the host cell the time to synthesize the polypeptide. Cultures are then typically frozen and may be stored frozen for some time, prior to isolation and purification of the polypeptide.

When using a prokaryotic host cell, the host cell may include a plasmid which expresses an internal T7 lysozyme, e.g., expressed from plasmid pLysSL (see Examples). Lysis of such host cells liberates the lysozyme which then degrades the bacterial membrane.

Other sequences that may be included in a vector for expression in bacterial or other prokaryotic cells include a synthetic ribosomal binding site; strong transcriptional terminators, e.g., t₀ from phage lambda and t₄ from the rrnB operon in E. coli, to prevent read through transcription and ensure stability of the expressed polypeptide; an origin of replication, e.g., ColE1; and beta-lactamase gene, conferring ampicillin resistance.

Other host cells include prokaryotic host cells. Even more preferred host cells are bacteria, e.g., E. coli. Other bacteria that can be used include Shigella spp., Salmonella spp., Listeria spp., Rickettsia spp., Yersinia spp., Escherichia spp., Klebsiella spp., Bordetella spp., Neisseria spp., Aeromonas spp., Francisella spp., Corynebacterium spp., Citrobacter spp., Chlamydia spp., Hemophilus spp., Brucella spp., Mycobacterium spp., Legionella spp., Rhodococcus spp., Pseudomonas spp., Helicobacter spp., Vibrio spp., Bacillus spp., and Erysipelothrix spp. Most of these bacteria can be obtained from the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, Va. 20110-2209).

A number of vectors exist for the expression of recombinant proteins in yeast. For instance, YEP24, YIP5, YEP51, YEP52, pYES2, and YRP17 are cloning and expression vehicles useful in the introduction of genetic constructs into S. cerevisiae (see, for example, Broach et al., (1983) in Experimental Manipulation of Gene Expression, ed. M. Inouye Academic Press, p. 83). These vectors may replicate in E. coli due to the presence of the pBR322 ori, and in S. cerevisiae due to the replication determinant of the yeast 2 micron plasmid. In addition, drug resistance markers such as ampicillin may be used.

In certain embodiments, mammalian expression vectors contain both prokaryotic sequences to facilitate the propagation of the vector in bacteria, and one or more eukaryotic transcription units that are expressed in eukaryotic cells. The pcDNAI/amp, pcDNAI/neo, pRc/CMV, pSV2gpt, pSV2neo, pSV2-dhfr, pTk2, pRSVneo, pMSG, pSVT7, pko-neo and pHyg derived vectors are examples of mammalian expression vectors suitable for transfection of eukaryotic cells. Some of these vectors are modified with sequences from bacterial plasmids, such as pBR322, to facilitate replication and drug resistance selection in both prokaryotic and eukaryotic cells. Alternatively, derivatives of viruses such as the bovine papilloma virus (BPV-1), or Epstein-Barr virus (pHEBo, pREP-derived and p205) can be used for transient expression of proteins in eukaryotic cells. The various methods employed in the preparation of the plasmids and transformation of host organisms are well known in the art. For other suitable expression systems for both prokaryotic and eukaryotic cells, as well as general recombinant procedures, see Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press, 1989) Chapters 16 and 17. In some instances, it may be desirable to express the recombinant protein by the use of a baculovirus expression system. Examples of such baculovirus expression systems include pVL-derived vectors (such as pVL1392, pVL1393 and pVL941), pAcUW-derived vectors (such as pAcUW1), and pBlueBac-derived vectors (such as the β-gal comprising pBlueBac III).

In another variation, protein production may be achieved using in vitro translation systems. In vitro translation systems are, generally, a translation system which is a cell-free extract comprising at least the minimum elements necessary for translation of an RNA molecule into a protein. An in vitro translation system typically comprises at least ribosomes, tRNAs, initiator methionyl-tRNAMet, proteins or complexes involved in translation, e.g., eIF2, eIF3, the cap-binding (CB) complex, comprising the cap-binding protein (CBP) and eukaryotic initiation factor 4F (eIF4F). A variety of in vitro translation systems are well known in the art and include commercially available kits. Examples of in vitro translation systems include eukaryotic lysates, such as rabbit reticulocyte lysates, rabbit oocyte lysates, human cell lysates, insect cell lysates and wheat germ extracts. Lysates are commercially available from manufacturers such as Promega Corp., Madison, Wis.; Stratagene, La Jolla, Calif.; Amersham, Arlington Heights, Ill.; and GIBCO/BRL, Grand Island, N.Y. In vitro translation systems typically comprise macromolecules, such as enzymes, translation, initiation and elongation factors, chemical reagents, and ribosomes. In addition, an in vitro transcription system may be used. Such systems typically comprise at least an RNA polymerase holoenzyme, ribonucleotides and any necessary transcription initiation, elongation and termination factors. An RNA nucleotide for in vitro translation may be produced using methods known in the art. In vitro transcription and translation may be coupled in a one-pot reaction to produce proteins from one or more isolated DNAs.

When expression of a carboxy terminal fragment of a polypeptide is desired, i.e. a truncation mutant, it may be necessary to add a start codon (ATG) to the oligonucleotide fragment comprising the desired sequence to be expressed. It is well known in the art that a methionine at the N-terminal position may be enzymatically cleaved by the use of the enzyme methionine aminopeptidase (MAP). MAP has been cloned from E. coli (Ben-Bassat et al., (1987) J. Bacteriol. 169:751-757) and Salmonella typhimurium and its in vitro activity has been demonstrated on recombinant proteins (Miller et al., (1987) PNAS USA 84:2718-1722). Therefore, removal of an N-terminal methionine, if desired, may be achieved either in vivo by expressing such recombinant polypeptides in a host which produces MAP (e.g., E. coli or CM89 or S. cerevisiae), or in vitro by use of purified MAP (e.g., procedure of Miller et al.).

In cases where plant expression vectors are used, the expression of a fusion protein may be driven by any of a number of promoters. For example, viral promoters such as the 35S RNA and 19S RNA promoters of CaMV (Brisson et al., 1984, Nature, 310:511-514), or the coat protein promoter of TMV (Takamatsu et al., 1987, EMBO J., 6:307-311) may be used; alternatively, plant promoters such as the small subunit of RUBISCO (Coruzzi et al., 1994, EMBO J., 3:1671-1680; Broglie et al., 1984, Science, 224:838-843); or heat shock promoters, e.g., soybean hsp 17.5-E or hsp 17.3-B (Gurley et al., 1986, Mol. Cell. Biol., 6:559-565) may be used. These constructs can be introduced into plant cells using Ti plasmids, Ri plasmids, plant virus vectors; direct DNA transformation; microinjection, electroporation, etc. For reviews of such techniques see, for example, Weissbach & Weissbach, 1988, Methods for Plant Molecular Biology, Academic Press, New York, Section VIII, pp. 421-463; and Grierson & Corey, 1988, Plant Molecular Biology, 2d Ed., Blackie, London, Ch. 7-9.

An alternative expression system which can be used to express a polypeptide tag or fusion protein comprising a polypeptide tag is an insect system. In one such system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes. The virus grows in Spodoptera frugiperda cells. The PGHS-2 sequence may be cloned into non-essential regions (for example the polyhedrin gene) of the virus and placed under control of an AcNPV promoter (for example the polyhedrin promoter). Successful insertion of the coding sequence will result in inactivation of the polyhedrin gene and production of non-occluded recombinant virus (i.e., virus lacking the proteinaceous coat coded for by the polyhedrin gene). These recombinant viruses are then used to infect Spodoptera frugiperda cells in which the inserted gene is expressed. (e.g., see Smith et al., 1983, J. Virol., 46:584, Smith, U.S. Pat. No. 4,215,051).

In a specific embodiment of an insect system, the DNA encoding fusion protein is cloned into the pBlueBacIII recombinant transfer vector (Invitrogen, San Diego, Calif.) downstream of the polyhedrin promoter and transfected into Sf9 insect cells (derived from Spodoptera frugiperda ovarian cells, available from Invitrogen, San Diego, Calif.) to generate recombinant virus. After plaque purification of the recombinant virus high-titer viral stocks are prepared that in turn would be used to infect Sf9 or High Five™ (BTI-TN-5B1-4 cells derived from Trichoplusia ni egg cell homogenates; available from Invitrogen, San Diego, Calif.) insect cells, to produce large quantities of appropriately post-translationally modified subject polypeptide.

In other embodiments, the components of any the fusion proteins of the invention are produced separately and then linked, e.g. covalently linked, to each other.

For example, an engineered mesothelin antibody or fragment thereof, and stress protein are produced separately in vitro, purified, and mixed together under conditions under which a tag, for example, a biotin or antibody binding protein, will be able to be linked to the polypeptide of interest. For example, the stress protein and/or the engineered mesothelin antibody or fragment thereof, can be obtained (isolated) from a source in which they are known to occur, can be produced and harvested from cell cultures, can be produced by cloning and expressing a gene encoding the desired stress protein or engineered mesothelin antibody, or can be synthesized chemically. Furthermore, a nucleic acid sequence encoding the desired stress protein or engineered mesothelin antibody or fragment thereof, or any component of the fusion proteins of the invention, can be synthesized chemically. Such mixtures of conjugated proteins may have properties different from single fusion proteins.

Linkers (also known as “linker molecules” or “cross-linkers”) may be used to conjugate the components of an fusion protein according to the invention. Linkers include chemicals able to react with a defined chemical group of several, usually two, molecules and thus conjugate them. The majority of known cross-linkers react with amine, carboxyl, and sulfhydryl groups. The choice of target chemical group is crucial if the group may be involved in the biological activity of the polypeptides to be conjugated. For example, maleimides, which react with sulfhydryl groups, may inactivate Cys-comprising peptides or proteins that require the Cys to bind to a target. Linkers may be homofunctional (comprising reactive groups of the same type), heterofunctional (comprising different reactive groups), or photoreactive (comprising groups that become reactive on illumination.

Linker molecules may be responsible for different properties of the conjugated compositions. The length of the linker should be considered in light of molecular flexibility during the conjugation step, and the availability of the conjugated molecule for its target (cell surface molecules and the like.) Longer linkers may thus improve the biological activity of the compositions of the present invention, as well as the ease of preparation of them. The geometry of the linker may be used to orient a molecule for optimal reaction with a target. A linker with flexible geometry may allow the cross-linked polypeptides to conformationally adapt as they bind other polypeptides. The nature of the linker may be altered for other various purposes. For example, the aryl-structure of MBuS was found to be less immunogenic than the aromatic spacer of MBS. Furthermore, the hydrophobicity and functionality of the linker molecules may be controlled by the physical properties of component molecules. For example, the hydrophobicity of a polymeric linker may be controlled by the order of monomeric units along the polymer, e.g. a block polymer in which there is a block of hydrophobic monomers interspersed with a block of hydrophilic monomers.

A linker or cross-linker that is useful according to the invention can facilitate proper folding of the fusion protein, improve the biological activity of the fusion proteins of the invention, can facilitate preparation of the fusion proteins of the invention etc. . . .

A linker can also function to provide for proper folding of the heavy and light chain segments of the scFv. A “linker” according to the invention may also contribute to target recognition.

Any suitable amino acid linker that does not interfere with proper protein folding and function is useful according to the invention.

In one embodiment, a linker is a combination of nucleic acids that yields a series of neutral or slightly polar amino acids that facilitates proper folding of the fusion protein

If an amino acid side chain cannot be ionized it is considered polar but neutral. For example, aspartate is polar and acidic because the carboxylic side chain can be ionized. Tyrosine is polar. The hydroxyl group on the phenyl ring is not easily ionized thus it is considered polar but neutral.

In one embodiment, a linker consists of nucleic acids encoding the following amino acid sequence: GGSSRSS (SEQ ID NO: 1). In another embodiment, the linker consists of nucleic acids encoding the following amino acid sequence: (GGGSGGG)×4 (SEQ ID NO: 2).

In another embodiment the linker sequence comprises the sequence (Gly4Ser)3 (SEQ ID NO: 3); GGGGSGGGGSGGGGS (SEQ ID NO: 3). It is preferable to include glycine in the linker sequence because it has an H-side chain whereas all other amino acids have bulkier side chains. Linkers include chemicals able to react with a defined chemical group of several, usually two, molecules and thus conjugate them. The majority of known cross-linkers react with amine, carboxyl, and sulfhydryl groups. The choice of target chemical group is crucial if the group may be involved in the biological activity of the proteins to be conjugated. For example, maleimides, which react with sulfhydryl groups, may inactivate Cys-comprising proteins that require the Cys to bind to a target. Linkers may be homofunctional (comprising reactive groups of the same type), heterofunctional (comprising different reactive groups), or photoreactive (comprising groups that become reactive on illumination).

Linker molecules may be responsible for different properties of the conjugated compositions. The length of the linker should be considered in light of molecular flexibility during the conjugation step, and the availability of the conjugated molecule for its target (cell surface molecules and the like.) Longer linkers may thus improve the biological activity of the compositions of the present invention, as well as the ease of preparation of them. The geometry of the linker may be used to orient a molecule for optimal reaction with a target. A linker with flexible geometry may allow the cross-linked proteins to conformationally adapt as they bind other proteins. The nature of the linker may be altered for other various purposes. For example, the aryl-structure of MBuS was found less immunogenic than the aromatic spacer of MBS. Furthermore, the hydrophobicity and functionality of the linker molecules may be controlled by the physical properties of component molecules. For example, the hydrophobicity of a polymeric linker may be controlled by the order of monomeric units along the polymer, e.g. a block polymer in which there is a block of hydrophobic monomers interspersed with a block of hydrophilic monomers.

The chemistry of preparing and utilizing a wide variety of molecular linkers is well-known in the art and many pre-made linkers for use in conjugating molecules are commercially available from vendors such as Pierce Chemical Co., Roche Molecular Biochemicals, United States Biological, and the like.

The prepared and/or isolated heat shock protein fused to a biotin-binding protein is to be administered to a subject in conjunction with the desired biotinylated components, sufficient to form a non-covalent association of the biotin moiety with the biotin-binding protein. The heat shock protein fusion and the biotinylated component or components may be administered simultaneously or sequentially. If administered simultaneously, the heat shock protein fusion and the biotinylated component or components may be administered as a mixture or as a noncovalent complex. If administered as a noncovalent complex, a heat shock protein fused to a biotin-binding protein may be noncovalently bound to the desired biotinylated components either in vitro or in vivo once prepared and/or isolated.

The chemistry of preparing and utilizing a wide variety of molecular linkers is well-known in the art and many pre-made linkers for use in conjugating molecules are commercially available from vendors such as Pierce Chemical Co., Roche Molecular Biochemicals, United States Biological, and the like.

3. Methods of Using the Fusion Proteins

The fusion proteins described herein can be administered to a subject to enhance that subject's immune response, particularly a cell-mediated cytolytic response, against a cell expressing mesothelin. The fusion protein may simply enhance the immune response (thus serving as an immunogenic composition), or confer protective immunity (thus serving as a vaccine).

Thus, the protein fusion polypeptides produced as described above may be purified to a suitable purity for use as a pharmaceutical composition. Generally, a purified composition will have one species that comprises more than about 85 percent of all species present in the composition, more than about 85%, 86%, 875, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more of all species present. The object species may be purified to essential homogeneity (contaminant species cannot be detected in the composition by conventional detection methods) wherein the composition consists essentially of a single species. A skilled artisan may purify a fusion protein using standard techniques for protein purification, for example, immunoaffinity chromotography, size exclusion chromatography, etc. in light of the teachings herein. Purity of a polypeptide may be determined by a number of methods known to those of skill in the art, including for example, amino-terminal amino acid sequence analysis, gel electrophoresis and mass-spectrometry analysis.

Accordingly, provided are pharmaceutical compositions comprising the above-described fusion proteins. In one aspect, provided are pharmaceutically acceptable compositions which comprise a therapeutically-effective amount of one or more of the compounds described above and below, formulated together with one or more pharmaceutically acceptable carriers (additives) and/or diluents. In another aspect, in certain embodiments, the compounds may be administered as such or in admixtures with pharmaceutically acceptable carriers and may also be administered in conjunction with other agents. Conjunctive (combination) therapy thus includes sequential, simultaneous and separate, or co-administration of the active compound in a way that the therapeutic effects of the first administered one has not entirely disappeared when the subsequent is administered.

The fusion proteins described herein can be administered to a subject in a variety of ways. The routes of administration include intradermal, transdermal (e.g., slow release polymers), intramuscular, intraperitoneal, intravenous, subcutaneous, oral, epidural and intranasal routes. Any other convenient route of administration can be used, for example, infusion or bolus injection, or absorption through epithelial or mucocutaneous linings. In addition, the compositions described herein can contain and be administered together with other pharmacologically acceptable components such as biologically active agents (e.g., adjuvants such as alum), surfactants (e.g., glycerides), excipients (e.g., lactose), carriers, diluents and vehicles. Furthermore, the compositions can be used ex vivo as a means of stimulating white blood cells obtained from a subject to elicit, expand and propagate antigen-specific immune cells in vitro that are subsequently reintroduced into the subject.

Further, a fusion protein can be administered by in vivo expression of a nucleic acid encoding such protein sequences into a human subject. Expression of such a nucleic acid can also be achieved ex vivo as a means of stimulating white blood cells obtained from a subject to elicit, expand and propagate mesothelin-specific immune cells in vitro that are subsequently reintroduced into the subject. Expression vectors suitable for directing the expression of a fusion protein of interest can be selected from the large variety of vectors currently used in the field. Preferred will be vectors that are capable of producing high levels of expression as well as are effective in transducing a gene of interest. For example, recombinant adenovirus vector pJM17 (All et al., Gene Therapy 1:367-84 (1994); Berkner K. L., Biotechniques 6:616-24 1988), second generation adenovirus vectors DE1/DE4 (Wang and Finer, Nature Medicine 2:714-6 (1996)), or adeno-associated viral vector AAV/Neo (Muro-Cacho et al., J. Immunotherapy 11:231-7 (1992)) can be used. Furthermore, recombinant retroviral vectors MFG (Jaffee et al., Cancer Res. 53:2221-6 (1993)) or LN, LNSX, LNCX, LXSN (Miller and Rosman, Biotechniques 7:980-9 (1989)) can be employed. Herpes simplex virus-based vectors such as pHSV1 (Geller et al., Proc. Nat'l Acad. Sci. 87:8950-4 (1990) or vaccinia viral vectors such as MVA (Sutter and Moss. Proc. Nat'l Acad. Sci. 89:10847-51 (1992)) can serve as alternatives.

Frequently used specific expression units including promoter and 3′ sequences are those found in plasmid CDNA3 (Invitrogen), plasmid AH5, pRC/CMV (Invitrogen), pCMU II (Paabo et al., EMBO J. 5:1921-1927 (1986)), pZip-Neo SV (Cepko et al., Cell 37:1053-1062 (1984)) and pSRa (DNAX, Palo Alto, Calif.). The introduction of genes into expression units and/or vectors can be accomplished using genetic engineering techniques, as described in manuals like Molecular Cloning and Current Protocols in Molecular Biology (Sambrook, J., et al., Molecular Cloning, Cold Spring Harbor Press (1989); Ausubel, F. M. et al., Current Protocols in Molecular Biology, Greene Publishing Associates and Wiley-Interscience (1989)). A resulting expressible nucleic acid can be introduced into cells of a human subject by any method capable of placing the nucleic acid into cells in an expressible form, for example as part of a viral vector such as described above, as naked plasmid or other DNA, or encapsulated in targeted liposomes or in erythrocyte ghosts (Friedman, T., Science, 244:1275-1281 (1989); Rabinovich, N. R. et al., Science. 265:1401-1404 (1994)). Methods of transduction include direct injection into tissues and tumors, liposomal transfection (Fraley et al., Nature 370:111-117 (1980)), receptor-mediated endocytosis (Zatloukal et al., Ann. N.Y. Acad. Sci. 660:136-153 (1992)), and particle bombardment-mediated gene transfer (Eisenbraun et al., DNA & Cell. Biol. 12:791-797 (1993)).

The amount of fusion polypeptide (fused, conjugated or noncovalently joined as discussed before) in the compositions of the present invention is an amount which produces an effective immunostimulatory response in a subject as determined by the methods described herein. An effective amount is an amount such that when administered, it induces an immune response. In addition, the amount of fusion protein administered to the subject will vary depending on a variety of factors, including the engineered antibody and stress protein employed, the size, age, body weight, general health, sex, and diet of the subject as well as on the subject's general immunological responsiveness. Adjustment and manipulation of established dose ranges are well within the ability of those skilled in the art. For example, the amount of engineered fusion protein according to the invention, for example, mesothelin antibody-stress protein fusion protein, can be from about 1 microgram to about 1 gram, preferably from about 100 microgram to about 1 gram, and from about 1 milligram to about 1 gram. An effective amount of a composition comprising an expression vector is an amount such that when administered, it induces an immune response against mesothelin against which the engineered antibody or fragment thereof, is directed. Furthermore, the amount of expression vector administered to the subject will vary depending on a variety of factors, including the engineered mesothelin antibody and stress protein expressed, the size, age, body weight, general health, sex, and diet of the subject, as well as on the subject's general immunological responsiveness. Additional factors that need to be considered are the route of application and the type of vector used. For example, when prophylactic or therapeutic treatment is carried out with a viral vector containing a nucleic acid encoding an engineered fusion protein according to the invention, the effective amount will be in the range of 10⁴ to 10¹² helper-free, replication-defective virus per kg body weight, preferably in the range of 10⁵ to 10¹¹ virus per kg body weight and most preferably in the range of 10⁶ to 10¹⁰ virus per kg body weight.

Fusion proteins of the invention can also be administered in combination with another factor. For example, a fusion protein comprising a stress protein fused to a biotin binding protein is administered with a biotinylated antibody or fragment thereof that binds specifically to mesothelin, to form a non-covalent interaction. In another embodiment, a fusion protein comprising a stress protein fused to an antibody binding protein is administered with an antibody or fragment thereof that binds specifically to mesothelin, to form a non-covalent interaction.

In one embodiment the ratio of stress protein-biotin binding protein fusion to biotinylated antibody or the ratio of stress protein-antibody binding protein to antibody is 1:1. The methods of the invention also include ratios of stress protein-biotin binding protein fusion to biotinylated antibody or the ratio of stress protein-antibody binding protein to antibody wherein the ratio is 1:1.1, 1:1.2, 1:1.3, 1:1.4, 1:1.5, 1:1.6, 1:1.7, 1:1.8, 1:1.9, 1:2, 1:2.5, 1:3, 1:3.5, 1:4, 1:5 or more.

4. Self-Assembling Vaccines

Multiple components may be administered in conjunction with a heat shock protein fusion as further described. For example, a fusion protein comprising a stress protein fused to either a biotin binding protein or an antibody binding protein can be administered in conjunction with a biotinylated antibody or fragment thereof that binds specifically to mesothelin or an antibody or fragment thereof that binds specifically to mesothelin, respectively. In this way, multivalent pharmaceutical compositions may be generated and administered to a subject. The generation of multivalent pharmaceutical compositions allow for the production of “supercharged,” or more potent vaccines and therapeutics. When the biotinylated component comprises an antibody, such vaccine exhibits activity improvement for marketed antibodies. Alternatively, an antibody that binds specifically to mesothelin can be used in combination with a stress protein fused to an antibody binding protein to produce a vaccine that exhibits increased activity.

Wherein the pharmaceutical composition is multivalent, the biotinylated components to be administered may be any combination of biotinylated components described herein. For example, biotinylated components of the same or different identities may be administered in conjunction with a heat shock protein fusion as provided herein, provided that the biotin-binding protein, and in turn the heat shock protein fusion, is multivalent, or capable of binding multiple biotinylated components. As an example, the wild-type biotin-binding protein avidin has four biotin-binding sites and is therefore capable of binding four biotinylated components. In this example, the four sites are to be bound by four biotinylated components, and the biotin-binding components may be mixed and matched based on identity in any possible permutation of one, two, three, or four identical biotinylated components described herein. Four identical biotinylated components may be bound to the four biotin-binding sites.

Therefore, an effective amount of a biotinylated component with a first identity may be may be administered to a subject in conjunction with a heat shock protein fused to a biotin-binding protein, sufficient to form a pharmaceutical composition comprising four parts biotinylated component of a first identity and one part heat shock protein fused to a biotin-binding protein. Alternatively, an effective amount of biotinylated components with a first and second identity may be may be administered to a subject in conjunction with a heat shock protein fused to a biotin-binding protein, sufficient to form a pharmaceutical composition comprising three parts biotinylated component of a first identity, one part biotinylated component of a second identity, and one part heat shock protein fusion. In another embodiment, an effective amount of biotinylated components with a first and second identity may be administered to a subject in conjunction with a heat shock protein fused to a biotin-binding protein, sufficient to form a pharmaceutical composition comprising two parts biotinylated component of a first identity, two parts biotinylated component of a second identity, and one part heat shock protein fusion.

Wherein the self-assembling pharmaceutical composition is divalent, an effective amount of biotinylated component of a first identity may be administered to a subject in conjunction with a heat shock protein fused to a biotin-binding protein, sufficient to form a pharmaceutical composition comprising two parts biotinylated component of a first identity and one part heat shock protein fusion. Alternatively, an effective amount of biotinylated components with a first and second identity may be administered to a subject in conjunction with a heat shock protein fused to a biotin-binding protein, sufficient to form a pharmaceutical composition comprising one part biotinylated component of a first identity, one part biotinylated component of a second identity, and one part heat shock protein fusion.

A biotinylated component of a multivalent pharmaceutical composition may include a costimulatory molecule, or a blocking group (i.e., biotin alone or biotin conjugated to a non-functional molecule). Examples of costimulatory molecules that may be administered in conjunction with the present invention include B7 molecules, including B7-1 (CD80) and B7-2 (CD86), CD28, CD58, LFA-3, CD40, B7-H3, CD137 (4-1BB), and interleukins (e.g., IL-1, IL-2, or IL-12). As an example, one part biotinylated component comprising a costimulatory molecule may be administered in conjunction with i) three parts of another biotinylated component comprising a protein, cell or virus; and ii) one part heat shock protein fused to a biotin-binding protein. In another example, two parts biotinylated component comprising a costimulatory molecule may be administered in conjunction with i) two parts of another biotinylated component comprising a protein, cell, or virus; and ii) one part heat shock protein fused to a biotin-binding protein. In another example, three parts biotinylated component comprising a costimulatory molecule may be administered in conjunction with i) one part of another biotinylated component comprising a protein, cell, or virus; and ii) one part heat shock protein fused to a biotin-binding protein.

A pH-sensitive mutant of avidin, streptavidin, or neutravidin, for example, may be employed to control the noncovalent interaction of avidin-, streptavidin-, or neutravidin-to biotin, and thereby achieve the desired stoichiometry of heat shock protein fusion with the various permutations and combinations of biotinylated component, as described herein. The choice of wild-type or a particular mutant form of biotin-binding protein such as avidin may be employed to control the desired valency of the pharmaceutical composition (e.g., monomeric, dimeric, or tetrameric form of avidin). Monovalent or divalent vaccines may be similarly produced by employing heat shock fusion proteins comprising other avidin, streptavidin, or neutravidin mutant proteins that bind biotin but in a monovalent or divalent fashion. An example of a pH-sensitive point mutant of Avidin which confers pH-adjustable biotin binding is Y33H. Another mutant has substitutions of histidine for Met96, Val115, and Ile117, optionally with histidine replacement at Trp110. Such approaches for controlling biotin-streptavidin binding are described in Laitinen, O. H. (2007), “Brave New (Strept)avidins in Biotechnology,” Trends in Biotechnology 25 (6): 269-277 and Nordlund, H. R. (2003), “Introduction of histidine residues into avidin subunit interfaces allows pH-dependent regulation of quaternary structure and biotin binding,” FEBS Letters 555: 449-454, the contents of both of which are incorporated herein by reference.

5. Methods of Producing the Self-Assembling Pharmaceutical Compositions

In one embodiment of the present invention, compositions are comprised of two moieties: a heat shock protein fused to a biotin-binding protein in combination with a biotinylated component which targets the immune response to the antigen to which the immune response is desired, for example, mesothelin. The present invention provides for fast, easy production of large amounts pharmaceutical composition (e.g., vaccine) because the production of biotinylated antigens or antibodies is well known and rapid, which, in turn, allows for an increased capacity for vaccine production. Because a heat shock protein fusion of a single identity may be administered in conjunction with any of a number of various biotinylated components as described herein, the heat shock fusion protein need not be synthesized de novo each time a new target antigen of interest is identified. Therefore, such methods of production are particularly rapid once the heat shock protein fusion to be administered is established and has been produced.

Methods for making the heat shock protein fused to a biotin-binding protein or antibody binding protein are described in detail hereinabove.

The heat shock protein may be prepared, using standard techniques, from natural sources, for example as described in Flynn et al., Science 245:385-390 (1989), or using recombinant techniques such as expression of a heat shock encoding gene construct in a suitable host cell such as a bacterial, yeast or mammalian cell. A fusion protein including the heat shock protein and biotin-binding protein can be produced by recombinant means. For example, a nucleic acid encoding the heat shock protein can be joined to either end of a nucleic acid sequence encoding the biotin-binding protein such that the two protein-coding sequences are sharing a common translational reading frame and can be expressed as a fusion protein including the biotin-binding protein and the heat shock protein. The combined sequence is inserted into a suitable vector chosen based on the expression features desired and the nature of the host cell. In the examples provided hereinafter, the nucleic acid sequences are assembled in a vector suitable for protein expression in the bacterium E. coli. Following expression in the chosen host cell, the fusion protein can be purified by routine biochemical separation techniques or by immunoaffinity methods using an antibody to one or the other part of the fusion protein. Alternatively, the selected vector can add a tag to the fusion protein sequence, e.g., an oligohistidine tag as described in the examples presented hereinafter, permitting expression of a tagged fusion protein that can be purified by affinity methods using an antibody or other material having an appropriately high affinity for the tag. Sambrook et al., Molecular Cloning: A Laboratory Manual, 2d Ed., Cold Spring Harbor Laboratory Press (1989); Deutscher, M. Guide to Protein Purification Methods Enzymology, vol. 182. Academic Press, Inc. San Diego, Calif. (1990). If a vector suitable for expression in mammalian cells is used. e.g., one of the vectors discussed below, the heat shock protein fusion can be expressed and purified from mammalian cells. Alternatively, the mammalian expression vector (including fusion protein-coding sequences) can be administered to a subject to direct expression of heat shock protein fusion protein in the subject's cells. A nucleic acid encoding a heat shock protein can also be produced chemically and then inserted into a suitable vector for fusion protein production and purification or administration to a subject. Finally, a fusion protein can also be prepared chemically.

Linkers (also known as “linker molecules” or “cross-linkers”) may be used to conjugate the components of any fusion protein according to the invention.

The invention also provides for linkers or cross-linkers that can be used to conjugate the two or more components of a fusion protein of the invention. Cross-linkers include chemicals able to react with a defined chemical group of several, usually two, molecules and thus conjugate them. The majority of known cross-linkers react with amine, carboxyl, and sulfhydryl groups. The choice of target chemical group is crucial if the group may be involved in the biological activity of the polypeptides to be conjugated. For example, maleimides, which react with sulfhydryl groups, may inactivate Cys-comprising peptides or proteins that require the Cys to bind to a target. Linkers may be homofunctional (comprising reactive groups of the same type), heterofunctional (comprising different reactive groups), or photoreactive (comprising groups that become reactive on illumination).

The prepared and/or isolated heat shock protein fused to a biotin-binding protein is to be administered to a subject in conjunction with the desired biotinylated components, sufficient to form a non-covalent association of the biotin moiety with the biotin-binding protein. The heat shock protein fusion and the biotinylated component or components may be administered simultaneously or sequentially. If administered simultaneously, the heat shock protein fusion and the biotinylated component or components may be administered as a mixture or as a noncovalent complex. If administered as a noncovalent complex, a heat shock protein fused to a biotin-binding protein may be noncovalently bound to the desired biotinylated components either in vitro or in vivo once prepared and/or isolated.

The noncovalent complex may be produced by contacting the heat shock protein fused to a biotin-binding protein with the biotinylated components, under conditions sufficient to promote the binding of the biotin-binding protein with biotin, which conditions are known in the art.

Genes for various heat shock proteins have been cloned and sequenced, and which may be used to obtain a heat shock protein fusion, including, but not limited to, gp96 (human: Genebank Accession No. X15187; Maki et al., Proc. Natl. Acad. Sci. U.S.A. 87:5658-5562 (1990); mouse: Genebank Accession No. M16370; Srivastava et al., Proc. Natl. Acad. Sci. U.S.A. 84:3807-3811 (1987)), BiP (mouse: Genebank Accession No. U16277; Haas et al., Proc. Natl. Acad. Sci. U.S.A. 85:2250-2254 (1988); human: Genebank Accession No. M19645; Ting et al., DNA 7:275-286 (1988)), hsp70 (mouse: Genebank Accession No. M35021; Hunt et al., Gene 87:199-204 (1990); human: Genebank Accession No. M24743; Hunt et al, Proc. Natl. Acad. Sci. U.S.A. 82:6455-6489 (1995)), and hsp40 (human: Genebank Accession No. D49547; Ohtsuka K., Biochem. Biophys. Res. Commun. 197:235-240 (1993)).

The heat shock protein fused to a biotin-binding protein may be non-covalently bound to the biotinylated component.

The component to be administered in conjunction with the heat shock protein comprising the protein, cell, or virus may be conjugated to biotin by means such as is known in the art. Prior to conjugation to biotin, the protein, cell, or virus may be produced and/or isolated using methods known in the art. Recombinant techniques may be employed in much the same way as described herein for the heat shock protein fusion. Once the component is produced and/or isolated, a biotin molecule or molecules may be conjugated directly to a protein, cell, or virus. Biotin may also be conjugated indirectly through a linker to said protein, cell, or virus. Biotin is to be conjugated to a region that sterically allows for the interaction of biotin with the biotin-binding protein. Biotinylation kits and reagents may be purchased from Pierce (Rockford, Ill.) and used to generate the biotinylated components described herein.

The sequences of many different antigens can be cloned and characterized by DNA sequence analysis and included in the compositions provided herein. Bacterial vectors containing complete or partial cellular or viral genomes or antigens may be obtained from various sources including, for example, the American Tissue Culture Collection (ATCC). Additional antigens which may be used can be isolated and typed by the methods previously established for this purpose, which methods are well known in the art.

6. Methods of Using the Heat Shock Protein Fusion and Biotinylated Components

The heat shock protein fusion and biotinylated components described herein can be administered to a subject to induce or enhance that subject's immune response, particularly a cell-mediated cytolytic response, against a cell expressing an antigen against which the biotinylated components are directed. The fusion protein may simply enhance the immune response (thus serving as an immunogenic composition), or confer protective immunity (thus serving as a vaccine).

Thus, the heat shock protein fusion and biotinylated components produced as described above may be purified to a suitable purity for use as a pharmaceutical composition. Generally, purified compositions will have one species that comprises more than about 85 percent of all species present in the composition, more than about 85%, 90%, 95%, 99% or more of all species present. The object species may be purified to essential homogeneity (contaminant species cannot be detected in the composition by conventional detection methods) wherein the composition consists essentially of a single species. A skilled artisan may purify a heat shock protein fusion and biotinylated components, or a non-covalent complex of the same, using standard techniques for purification, for example, immunoaffinity chromotography, size exclusion chromatography, etc. in light of the teachings herein. Purity of a protein may be determined by a number of methods known to those of skill in the art, including for example, amino-terminal amino acid sequence analysis, gel electrophoresis and mass-spectrometry analysis.

Accordingly, provided are pharmaceutical compositions comprising the above-described heat shock protein fusion and biotinylated components, or a non-covalent complex of the same. In one aspect, provided are pharmaceutically acceptable compositions which comprise a therapeutically-effective amount of one or more of the pharmaceutical compositions described herein, formulated together with one or more pharmaceutically acceptable carriers (additives) and/or diluents. In another aspect, in certain embodiments, the pharmaceutical compositions may be administered as such or in admixtures with pharmaceutically acceptable carriers and may also be administered in conjunction with other agents. Conjunctive (combination) therapy thus includes sequential, simultaneous and separate, or co-administration in a way that the therapeutic effects of the first administered one has not entirely disappeared when the subsequent is administered.

The heat shock protein fusion and biotinylated components, or components bound to an antibody-binding protein, or a non-covalent complex of the same, as described herein can be administered to a subject in a variety of ways. The routes of administration include systemic, peripheral, parenteral, enteral, topical, and transdermal (e.g., slow release polymers). Any other convenient route of administration can be used, for example, infusion or bolus injection, or absorption through epithelial or mucocutaneous linings. In addition, the compositions described herein can contain and be administered together with or without other pharmacologically acceptable components such as biologically active agents (e.g., adjuvants such as alum), surfactants (e.g., glycerides), excipients (e.g., lactose), carriers, diluents and vehicles. Furthermore, the compositions can be used ex vivo as a means of stimulating white blood cells obtained from a subject to elicit, expand and propagate antigen-specific immune cells in vitro that are subsequently reintroduced into the subject.

Further, a heat shock protein fusion protein can be administered by in vivo expression of a nucleic acid encoding such protein sequences into a human subject. Expression of such a nucleic acid and contact with biotinylated components can also be achieved ex vivo as a means of stimulating white blood cells obtained from a subject to elicit, expand and propagate antigen-specific immune cells in vitro that are subsequently reintroduced into the subject. Expression vectors suitable for directing the expression of heat shock protein fusion proteins can be selected from the large variety of vectors currently used in the field. Preferred will be vectors that are capable of producing high levels of expression as well as are effective in transducing a gene of interest. For example, recombinant adenovirus vector pJM17 (All et al., Gene Therapy 1:367-84 (1994); Berkner K. L., Biotechniques 6:616-24 1988), second generation adenovirus vectors DE1/DE4 (Wang and Finer, Nature Medicine 2:714-6 (1996)), or adeno-associated viral vector AAV/Neo (Muro-Cacho et al., J. Immunotherapy 11:231-7 (1992)) can be used. Furthermore, recombinant retroviral vectors MFG (Jaffee et al., Cancer Res. 53:2221-6 (1993)) or LN, LNSX, LNCX, LXSN (Miller and Rosman, Biotechniques 7:980-9 (1989)) can be employed. Herpes simplex virus-based vectors such as pHSV1 (Geller et al., Proc. Nat'l Acad. Sci. 87:8950-4 (1990) or vaccinia viral vectors such as MVA (Sutter and Moss. Proc. Nat'l Acad. Sci. 89:10847-51 (1992)) can serve as alternatives.

Frequently used specific expression units including promoter and 3′ sequences are those found in plasmid CDNA3 (Invitrogen), plasmid AH5, pRC/CMV (Invitrogen), pCMU II (Paabo et al., EMBO J. 5:1921-1927 (1986)), pZip-Neo SV (Cepko et al., Cell 37:1053-1062 (1984)) and pSRa (DNAX, Palo Alto, Calif.). The introduction of genes into expression units and/or vectors can be accomplished using genetic engineering techniques, as described in manuals like Molecular Cloning and Current Protocols in Molecular Biology (Sambrook, J., et al., Molecular Cloning, Cold Spring Harbor Press (1989); Ausubel, F. M. et al., Current Protocols in Molecular Biology, Greene Publishing Associates and Wiley-Interscience (1989)). A resulting expressible nucleic acid can be introduced into cells of a human subject by any method capable of placing the nucleic acid into cells in an expressible form, for example as part of a viral vector such as described above, as naked plasmid or other DNA, or encapsulated in targeted liposomes or in erythrocyte ghosts (Friedman, T., Science, 244:1275-1281 (1989); Rabinovich, N. R. et al., Science. 265:1401-1404 (1994)). Methods of transduction include direct injection into tissues and tumors, liposomal transfection (Fraley et al., Nature 370:111-117 (1980)), receptor-mediated endocytosis (Zatloukal et al., Ann. N.Y. Acad. Sci. 660:136-153 (1992)), and particle bombardment-mediated gene transfer (Eisenbraun et al., DNA & Cell. Biol. 12:791-797 (1993)).

The amount of heat shock protein fusion and biotinylated components, or a non-covalent complex of the same, in the compositions of the present invention is an amount which produces an effective immunostimulatory response in a subject. An effective amount is an amount such that when administered, it induces an immune response. In addition, the amount of heat shock protein fusion and biotinylated components, or a non-covalent complex of the same, administered to the subject will vary depending on a variety of factors, including the heat shock protein fusion and biotinylated component employed, the size, age, body weight, general health, sex, and diet of the subject as well as on the subject's general immunological responsiveness. Adjustment and manipulation of established dose ranges are well within the ability of those skilled in the art. For example, the amount of heat shock protein fusion, biotinylated components, or a non-covalent complex of the same can be from about 1 microgram to about 1 gram, preferably from about 100 microgram to about 1 gram, and from about 1 milligram to about 1 gram. An effective amount of a composition comprising an expression vector is an amount such that when administered, it induces an immune response against the antigen against which the pharmaceutical composition is directed. Furthermore, the amount of expression vector administered to the subject will vary depending on a variety of factors, including the heat shock protein fusion expressed, the size, age, body weight, general health, sex, and diet of the subject, as well as on its general immunological responsiveness. Additional factors that need to be considered are the route of application and the type of vector used. For example, when prophylactic or therapeutic treatment is carried out with a viral vector containing a nucleic acid encoding heat shock protein fusion, the effective amount will be in the range of 10⁴ to 10¹² helper-free, replication-defective virus per kg body weight, preferably in the range of 10⁵ to 10¹¹ virus per kg body weight and most preferably in the range of 10⁶ to 10¹⁰ virus per kg body weight.

Determination of an effective amount of fusion protein and biotinylated components, or a non-covalent complex of the same, for inducing an immune response in a subject is well within the capabilities of those skilled in the art, especially in light of the detailed disclosure provided herein.

An effective dose can be estimated initially from in vitro assays. For example, a dose can be formulated in animal models to achieve an induction of an immune response using techniques that are well known in the art. One having ordinary skill in the art could readily optimize administration to humans based on animal data. Dosage amount and interval may be adjusted individually. For example, when used as a vaccine, the proteins and/or strains of the invention may be administered in about 1 to 3 doses for a 1-36 week period. Preferably, 3 doses are administered, at intervals of about 3-4 months, and booster vaccinations may be given periodically thereafter. Alternate protocols may be appropriate for individual patients. A suitable dose is an amount of protein or strain that, when administered as described above, is capable of raising an immune response in an immunized patient sufficient to protect the patient from the condition or infection for at least 1-2 years.

The compositions may also include adjuvants to enhance immune responses. In addition, such proteins may be further suspended in an oil emulsion to cause a slower release of the proteins in vivo upon injection. The optimal ratios of each component in the formulation may be determined by techniques well known to those skilled in the art.

Any of a variety of adjuvants may be employed in the vaccines of this invention to enhance the immune response. Most adjuvants contain a substance designed to protect the antigen from rapid catabolism, such as aluminum hydroxide or mineral oil, and a specific or nonspecific stimulator of immune responses, such as lipid A, or Bortadella pertussis. Suitable adjuvants are commercially available and include, for example, Freund's Incomplete Adjuvant and Freund's Complete Adjuvant (Difco Laboratories) and Merck Adjuvant 65 (Merck and Company, Inc., Rahway, N.J.). Other suitable adjuvants include alum, biodegradable microspheres, monophosphoryl lipid A, quil A, SBAS1c, SBAS2 (Ling et al., 1997, Vaccine 15:1562-1567), SBAS7, Al(OH)₃ and CpG oligonucleotide (WO96/02555).

In the vaccines of the present invention, the adjuvant may induce a Th1 type immune response. Suitable adjuvant systems include, for example, a combination of monophosphoryl lipid A, preferably 3-de-O-acylated monophosphoryl lipid A (3D-MPL) together with an aluminum salt. An enhanced system involves the combination of a monophosphoryl lipid A and a saponin derivative, particularly the combination of 3D-MLP and the saponin QS21 as disclosed in WO 94/00153, or a less reactogenic composition where the QS21 is quenched with cholesterol as disclosed in WO 96/33739. Previous experiments have demonstrated a clear synergistic effect of combinations of 3D-MLP and QS21 in the induction of both humoral and Th1 type cellular immune responses. A particularly potent adjuvant formation involving QS21, 3D-MLP and tocopherol in an oil-in-water emulsion is described in WO 95/17210 and may comprise a formulation.

7. Kits

The present invention provides kits for expressing an engineered fusion protein according to the invention. Such kits may be comprised of nucleic acids encoding an engineered fusion protein of the invention. The nucleic acids may be included in a plasmid or a vector, e.g., a bacterial plasmid or viral vector. Other kits comprise an engineered fusion polypeptide. Furthermore, the present invention provides kits for producing and/or purifying fusion polypeptides according to the invention.

The present invention provides kits for expressing or administering a fusion protein of the invention, either alone or in combination with a biotinylated or non-biotinylated antibody or fragment thereof that binds specifically to mesothelin. Such kits may be comprised of nucleic acids encoding the fusion protein of interest. The nucleic acids may be included in a plasmid or a vector, e.g., a bacterial plasmid or viral vector. Other kits comprise a heat shock protein fused to a biotin-binding protein or an antibody-binding protein. Furthermore, the present invention provides kits for producing and/or purifying a fusion protein of the invention. Such kits may optionally include biotinylated components or biotinylation reagents as described herein.

The present invention provides kits for preventing or treating infectious, inflammatory, autoimmune or malignant disease in a patient. For example, a kit may comprise one or more pharmaceutical compositions as described above and optionally instructions for their use. In still other embodiments, the invention provides kits comprising one more pharmaceutical composition and one or more devices for accomplishing administration of such compositions.

Kit components may be packaged for either manual or partially or wholly automated practice of the foregoing methods. In other embodiments involving kits, instructions for their use may be provided.

EXAMPLES Example 1 Production of MTBhsp70/Huhsp70-Anti-Mesothelin Constructs

A fusion protein comprising a stress protein and an engineered mesothelin antibody can be prepared as follows. The anti-mesothelin scFv or mAb fragment is cloned, in frame, at the N-terminal end of a heat shock protein. The sequence encoding the scFv or mAb fragment can be separated from the N-terminus of the heat shock protein by a linker segment (for example a linker comprising (G4S)×3SEQ ID NO: 3).) Similarly, the construct is designed such that the scFv or the mAb fragment is cloned, in frame, at the C-terminal end of a heat shock protein, either directly or via a linker segment located between the heat shock protein C-terminal end and the scFv N-terminal segment. A sample scheme of this approach is depicted in FIG. 18A. FIG. 18B depicts the protein product of the construct described in this example.

Example 2 Production of Mesothelin Antibody (scFv) Binding Protein or Biotin-Binding Protein MTBhsp70/Huhsp70 Constructs

The invention provides for constructs that encode 1) engineered mesothelin antibody-stress protein-biotin-binding protein fusions and 2) engineered mesothelin antibody-stress protein-antibody binding protein fusion proteins.

These constructs are designed such that an scFv or Ab binding protein (or peptide) such as Protein A, Protein G, Protein L, or a biotin-binding protein (Avidin, Streptavidin etc.), is cloned, in frame, at the N-terminal end of a heat shock protein. A linker segment may or may not be added between the C-terminal of the scFv/Ab binding protein or of the biotin-binding protein and the N-terminal of the heat shock protein.

In one embodiment the linker is (G4S)×3 (SEQ ID NO: 3).

Alternatively, a construct according to the invention comprises an scFv/Ab binding protein segment or a biotin-binding segment inserted at the C-terminal end of the heat shock protein with or without a linker segment between the C-terminus of the heat shock protein and the N-terminus of the scFv/Ab binding protein segment.

The invention also includes but is not limited to the following linkers. In one embodiment, a linker segment comprises the hinge region from a member of the immunoglobulin gene family such as the CD8α chain depicted below.

Species Amino Acid Sequences of CD8α chain Hinge region SEQ ID NO Human DFLPTTAQPTKKSTLKKRVCRLPRPETQKGPLCSP 5 Guinea pig DVLPTTAQPTTKTTPKKKKCQPPSPGPQKGLHCSL 6 Chicken DVLPPLPSMSTLVPLTKKPMRCKPKNKAINKKGACTP 7 Axolot1 DSFPTTAILTTSTPCVGCKEHEETSKGSTKKKGARAGVACSS 8 rainbow trout ETRPTLTPVTKPKPPGIPTGRCTKRNYQTPEGCGY 9 br. trout ETRPTLTPVTKPKPPGIPTGRCTKRNDQTPKGCGS 10 salmon ETRPTLTPVTKPKPPRIPTGRCTKRNDQTPKGCGS 11 Adapted from Moore et al. (Characterization of salmon and trout CD8a and CD8β. Mol Immunol (2005)).

The constructs described herein and the resulting protein product are depicted in FIGS. 19A and 19B, respectively.

Example 3 Production of a Self-Assembling Vaccine

A self-assembling vaccine is prepared by reconstituting a lyophilized biotin-binding protein by the addition of biotinylated peptides, scFv, monoclonal antibodies, cells, and the like. The self-assembling vaccine can be administered to a subject, for example, via subcutaneous injection or intravenously, to induce an immune response. Alternatively, the self-assembling vaccine is administered via sublingual or nasal methods.

Example 4 Induction of an Immune Response

The fusion proteins of the invention are used to induce an immune response to mesothelin in an subject. In one embodiment, the anti-mesothelin antibody-stress protein is injected subcutaneously or intravenously to target tumors expressing high levels of mesothelin on the surface. An immune response to mesothelin is detected by any of the methods described herein, for example by ELISA or by immunohistochemical methods. 

I claim:
 1. A method for inducing an immune response to mesothelin in a subject comprising administering to the subject a fusion protein comprising a stress protein fused in frame with an engineered antibody or fragment thereof, that binds specifically to mesothelin to induce an immune response.
 2. A method of treating cancer in a subject, comprising administering to the subject a fusion protein comprising a stress protein fused in frame with an engineered antibody or fragment thereof, that binds specifically to mesothelin to treat cancer, wherein the cancer is characterized by overexpression of mesothelin in cancer cells.
 3. A method for inducing an immune response to mesothelin in a subject, comprising administering to said subject a fusion protein comprising a stress protein fused in frame with a biotin-binding protein in combination with a biotinylated engineered antibody or fragment thereof, that binds specifically to mesothelin, to induce an immune response.
 4. A method of treating cancer in a subject, comprising administering to said subject a fusion protein comprising a stress protein fused in frame with a biotin-binding protein in combination with a biotinylated engineered antibody or fragment thereof, that binds specifically to mesothelin, to treat cancer, wherein the cancer is characterized by overexpression of mesothelin in cancer cells.
 5. A method for inducing an immune response to mesothelin in a subject, comprising administering to said subject a fusion protein comprising an engineered antibody or fragment thereof, that binds specifically to mesothelin, fused in frame with a biotin binding protein to induce an immune response.
 6. A method of treating cancer in a subject, comprising administering to said subject a fusion protein comprising an engineered antibody or fragment thereof, that binds specifically to mesothelin fused in frame with a biotin binding protein to treat cancer, wherein the cancer is characterized by overexpression of mesothelin in cancer cells.
 7. The method of any one of claims 1-4 wherein the biotin-binding protein is selected from the group consisting of avidin, streptavidin, and neuravidin.
 8. The method of any one of claims 1-4, wherein said biotin-binding protein is non-covalently bound to a biotinylated component.
 9. The method of any one of claims 1-4, wherein the biotin binding protein is non-covalently bound to four biotinylated components, and further wherein at least two of the four biotinylated components are not identical.
 10. The method of claim 9, wherein at least one of the four biotinylated components is a costimulatory molecule.
 11. The method of anyone of claims 1-4, wherein said fusion protein further comprises a linker.
 12. The method of claim 11, wherein said linker comprises an amino acid sequence selected from the group consisting of: GGSSRSSSEQ ID NO: 1), (GGGSGGG)×4 (SEQ ID NO: 2), or GGGGSGGGGSGGGGS (SEQ ID NO: 3).
 13. A method for inducing an immune response to mesothelin in a subject, comprising administering to said subject a fusion protein comprising a stress protein fused in frame with an antibody binding protein in combination with an engineered antibody or fragment thereof, that binds specifically to mesothelin, to induce an immune response.
 14. A method of treating cancer in a subject, comprising administering to said subject a fusion protein comprising a stress protein fused in frame with an antibody binding protein in combination with an engineered antibody or fragment thereof, that binds specifically to mesothelin, to treat cancer, wherein the cancer is characterized by overexpression of mesothelin in cancer cells.
 15. A method for inducing an immune response to mesothelin in a subject, comprising administering to said subject a fusion protein comprising an engineered antibody or fragment thereof that binds specifically to mesothelin and an antibody binding protein, wherein the engineered antibody or fragment thereof is fused in frame with the antibody binding protein, to thereby induce an immune response.
 16. A method of treating cancer in a subject, comprising administering to said subject a fusion protein comprising an engineered antibody or fragment thereof, that binds specifically to mesothelin fused in frame with an antibody binding protein to treat cancer, wherein the cancer is characterized by overexpression of mesothelin in cancer cells.
 17. The method of claim 13 or 14, wherein said antibody binding protein is selected from the group consisting of: protein A, protein G, protein A/G and protein L.
 18. The method of anyone of claims 13-14, wherein said fusion protein comprises a linker.
 19. The method of claim 18, wherein said linker comprises an amino acid sequence selected from the group consisting of: GGSSRSSSEQ ID NO: 1), (GGGSGGG)×4 (SEQ ID NO: 2), or GGGGSGGGGSGGGGS (SEQ ID NO: 3).
 20. The method of claim 2, wherein the cancer is selected from the group consisting of mesothelioma, pancreatic adenocarcinoma, ovarian cancer, lung adenocarcinoma, meningioma, glioma, metastasis to the leptomininges, uterine adenocarcinoma, malignant mesothelioma, and pancreatic cancer.
 21. The method of claim 4, wherein the cancer is selected from the group consisting of mesothelioma, pancreatic adenocarcinoma, ovarian cancer, lung adenocarcinoma, meningioma, glioma, metastasis to the leptomininges, uterine adenocarcinoma, malignant mesothelioma, and pancreatic cancer.
 22. The method of claim 6, wherein the cancer is selected from the group consisting of mesothelioma, pancreatic adenocarcinoma, ovarian cancer, lung adenocarcinoma, meningioma, glioma, metastasis to the leptomininges, uterine adenocarcinoma, malignant mesothelioma, and pancreatic cancer.
 23. The method of claim 14, wherein the cancer is selected from the group consisting of mesothelioma, pancreatic adenocarcinoma, ovarian cancer, lung adenocarcinoma, meningioma, glioma, metastasis to the leptomininges, uterine adenocarcinoma, malignant mesothelioma, and pancreatic cancer.
 24. The method of claim 16, wherein the cancer is selected from the group consisting of mesothelioma, pancreatic adenocarcinoma, ovarian cancer, lung adenocarcinoma, meningioma, glioma, metastasis to the leptomininges, uterine adenocarcinoma, malignant mesothelioma, and pancreatic cancer. 